GSE51088: POSTN/TGFBI-associated stromal signature predicts poor...
In MetaGxOvarian: Transcriptomic Ovarian Cancer Datasets
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Description
To identify molecular prognosticators and therapeutic targets for high-grade serous epithelial ovarian cancers (EOCs) using genetic analyses driven by biologic features of EOC pathogenesis.Ovarian tissue samples (n = 172; 122 serous EOCs, 30 other EOCs, 20 normal/benign) collected prospectively from sequential patients undergoing gynecologic surgery were analyzed using RNA expression microarrays. Samples were classified based on expression of genes with potential relevance in ovarian cancer. Gene sets were defined using Rosetta Similarity Search Tool (ROAST) and analysis of variance (ANOVA). Gene copy number variations were identified by array comparative genomic hybridization.No distinct subgroups of EOC could be identified by unsupervised clustering, however, analyses based on genes correlated with periostin (POSTN) and estrogen receptor-alpha (ESR1) yielded distinct subgroups. When 95 high-grade serous EOCs were grouped by genes based on ANOVA comparing ESR1/WT1 and POSTN/TGFBI samples, overall survival (OS) was significantly shorter for 43 patients with tumors expressing genes associated with POSTN/TGFBI compared to 52 patients with tumors expressing genes associated with ESR1/WT1 (median 30 versus 49 months, respectively; P = 0.022). Several targets with therapeutic potential were identified within each subgroup. BRCA germline mutations were more frequent in the ESR1/WT1 subgroup. Proliferation-associated genes and TP53 status (mutated or wild-type) did not correlate with survival. Findings were validated using independent ovarian cancer datasets.Two distinct molecular subgroups of high-grade serous EOCs based on POSTN/TGFBI and ESR1/WT1 expressions were identified with significantly different OS. Specific differentially expressed genes between these subgroups provide potential prognostic and therapeutic targets.Copyright ?? 2013 Elsevier Inc. All rights reserved.
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experimentData(eset):
Experiment data
Experimenter name: Karlan BY, Dering J, Walsh C, Orsulic S, Lester J, Anderson LA, Ginther CL, Fejzo M, Slamon D
Laboratory: Karlan, Slamon 2014
Contact information:
Title: POSTN/TGFBI-associated stromal signature predicts poor prognosis in serous epithelial ovarian cancer.
URL:
PMIDs: 24368280
Abstract: A 250 word abstract is available. Use 'abstract' method.
Information is available on: preprocessing
notes:
platform_title:
Agilent-012097 Human 1A Microarray (V2) G4110B (Probe Name version)
platform_shorttitle:
Agilent G4110B
platform_summary:
hgug4110b
platform_manufacturer:
Agilent
platform_distribution:
commercial
platform_accession:
GPL7264
platform_technology:
in situ oligonucleotide
version:
2015-09-22 20:05:48
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: A_23_P100001 A_23_P100011 ... A_23_P99996 (18703 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
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assayData: 18703 features, 172 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
20 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
152.00 112.00 4.13 3.50 4.92
---------------------------
Available sample meta-data:
---------------------------
alt_sample_name:
Ov_Tumor_Ref_Mix vs. CS-OV-001 Ov_Tumor_Ref_Mix vs. CS-OV-002
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-003 Ov_Tumor_Ref_Mix vs. CS-OV-004
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-005 Ov_Tumor_Ref_Mix vs. CS-OV-006
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-007 Ov_Tumor_Ref_Mix vs. CS-OV-008
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-009 Ov_Tumor_Ref_Mix vs. CS-OV-010
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-011 Ov_Tumor_Ref_Mix vs. CS-OV-012
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-013 Ov_Tumor_Ref_Mix vs. CS-OV-014
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-015 Ov_Tumor_Ref_Mix vs. CS-OV-016
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-017 Ov_Tumor_Ref_Mix vs. CS-OV-018
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-019 Ov_Tumor_Ref_Mix vs. CS-OV-020
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-021 Ov_Tumor_Ref_Mix vs. CS-OV-022
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-023 Ov_Tumor_Ref_Mix vs. CS-OV-024
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-025 Ov_Tumor_Ref_Mix vs. CS-OV-026
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-027 Ov_Tumor_Ref_Mix vs. CS-OV-028
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-029 Ov_Tumor_Ref_Mix vs. CS-OV-030
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-031 Ov_Tumor_Ref_Mix vs. CS-OV-032
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-033 Ov_Tumor_Ref_Mix vs. CS-OV-034
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-035 Ov_Tumor_Ref_Mix vs. CS-OV-036
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-037 Ov_Tumor_Ref_Mix vs. CS-OV-038
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-039 Ov_Tumor_Ref_Mix vs. CS-OV-040
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-041 Ov_Tumor_Ref_Mix vs. CS-OV-042
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-043 Ov_Tumor_Ref_Mix vs. CS-OV-044
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-045 Ov_Tumor_Ref_Mix vs. CS-OV-046
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-047 Ov_Tumor_Ref_Mix vs. CS-OV-048
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-049 Ov_Tumor_Ref_Mix vs. CS-OV-050
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-051 Ov_Tumor_Ref_Mix vs. CS-OV-052
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-053 Ov_Tumor_Ref_Mix vs. CS-OV-054
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-055 Ov_Tumor_Ref_Mix vs. CS-OV-056
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-057 Ov_Tumor_Ref_Mix vs. CS-OV-058
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-059 Ov_Tumor_Ref_Mix vs. CS-OV-060
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-061 Ov_Tumor_Ref_Mix vs. CS-OV-062
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-063 Ov_Tumor_Ref_Mix vs. CS-OV-064
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-065 Ov_Tumor_Ref_Mix vs. CS-OV-066
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-067 Ov_Tumor_Ref_Mix vs. CS-OV-068
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-069 Ov_Tumor_Ref_Mix vs. CS-OV-070
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-071 Ov_Tumor_Ref_Mix vs. CS-OV-072
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-073 Ov_Tumor_Ref_Mix vs. CS-OV-074
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-075 Ov_Tumor_Ref_Mix vs. CS-OV-076
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-077 Ov_Tumor_Ref_Mix vs. CS-OV-078
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-079 Ov_Tumor_Ref_Mix vs. CS-OV-080
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-081 Ov_Tumor_Ref_Mix vs. CS-OV-082
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-083 Ov_Tumor_Ref_Mix vs. CS-OV-084
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-085 Ov_Tumor_Ref_Mix vs. CS-OV-086
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-087 Ov_Tumor_Ref_Mix vs. CS-OV-088
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-089 Ov_Tumor_Ref_Mix vs. CS-OV-090
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-091 Ov_Tumor_Ref_Mix vs. CS-OV-092
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-093 Ov_Tumor_Ref_Mix vs. CS-OV-094
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-095 Ov_Tumor_Ref_Mix vs. CS-OV-096
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-097 Ov_Tumor_Ref_Mix vs. CS-OV-098
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-099 (Other)
1 73
sample_type:
benign borderline healthy metastatic tumor
5 12 15 17 123
histological_type:
clearcell endo mucinous other ser NA's
3 7 9 11 122 20
summarygrade:
high low NA's
119 30 23
summarystage:
early late NA's
31 120 21
tumorstage:
1 2 3 4 NA's
22 9 103 17 21
substage:
a b c NA's
17 22 94 39
grade:
0 1 2 3 NA's
8 8 14 119 23
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
26.0 49.0 57.5 58.6 68.0 91.0
neo:
n
172
recurrence_status:
norecurrence recurrence NA's
36 111 25
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30 791 1491 1835 2344 7001 20
vital_status:
deceased living NA's
112 40 20
percent_normal_cells:
30- NA's
140 32
percent_stromal_cells:
30- NA's
140 32
percent_tumor_cells:
70+ NA's
140 32
uncurated_author_metadata:
title: Ov_Tumor_Ref_Mix vs. CS-OV-001///geo_accession: GSM1238145///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-001///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.8///characteristics_ch2.3: age at surgery: 50.45///characteristics_ch2.4: histology: MMMT///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 7///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238145/GSM1238145_US22502615_251209750932_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-002///geo_accession: GSM1238146///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-002///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.5///characteristics_ch2.3: age at surgery: 75.69///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 26///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238146/GSM1238146_US22502615_251209754104_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-003///geo_accession: GSM1238147///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-003///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 39.66///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 1///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 103///characteristics_ch2.9: disease status: Unknown///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238147/GSM1238147_US22502615_251209750994_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-004///geo_accession: GSM1238148///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-004///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.2///characteristics_ch2.3: age at surgery: 69.33///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 33///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238148/GSM1238148_US22502615_251209747186_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-005///geo_accession: GSM1238149///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-005///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.5///characteristics_ch2.3: age at surgery: 82.01///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIB///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 54///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238149/GSM1238149_US22502615_251209749503_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-006///geo_accession: GSM1238150///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-006///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 7.5///characteristics_ch2.3: age at surgery: 58.56///characteristics_ch2.4: histology: Adenocarcinoma///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 41///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238150/GSM1238150_US22502615_251209747514_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-007///geo_accession: GSM1238151///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-007///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.3///characteristics_ch2.3: age at surgery: 69.32///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIB///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 6///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238151/GSM1238151_US22502615_251209754110_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-008///geo_accession: GSM1238152///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-008///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 63.54///characteristics_ch2.4: histology: MMMT///characteristics_ch2.5: Stage: IIB///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 9///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238152/GSM1238152_US22502615_251209750954_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-009///geo_accession: GSM1238153///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-009///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.2///characteristics_ch2.3: age at surgery: 67.91///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 22///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238153/GSM1238153_US22502615_251209754145_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-010///geo_accession: GSM1238154///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-010///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 85.58///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 9///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238154/GSM1238154_US22502615_251209749837_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-011///geo_accession: GSM1238155///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-011///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 39.50///characteristics_ch2.4: histology: Mucinous///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 0///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 67///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238155/GSM1238155_US22502615_251209754811_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-012///geo_accession: GSM1238156///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-012///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 7.9///characteristics_ch2.3: age at surgery: 68.16///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 42///characteristics_ch2.9: disease status: Unknown///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238156/GSM1238156_US22502615_251209754098_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-013///geo_accession: GSM1238157///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-013///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.9///characteristics_ch2.3: age at surgery: 44.95///characteristics_ch2.4: histology: Normal///characteristics_ch2.5: tissue status: Benign///characteristics_ch2.6: disease status: Benign///characteristics_ch2.7: patient status: Benign///characteristics_ch2.8: disease state: Normal ovarian///characteristics_ch2.9: ///characteristics_ch2.10: ///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Normal_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238157/GSM1238157_US22502615_251209747185_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-014///geo_accession: GSM1238158///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-014///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9///characteristics_ch2.3: age at surgery: 59.66///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 66///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238158/GSM1238158_US22502615_251209751008_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-015///geo_accession: GSM1238159///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-015///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.2///characteristics_ch2.3: age at surgery: 62.28///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 73///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238159/GSM1238159_US22502615_251209754814_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-016///geo_accession: GSM1238160///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-016///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.2///characteristics_ch2.3: age at surgery: 90.78///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: grade: unknown///characteristics_ch2.6: tissue status: Primary///characteristics_ch2.7: follow up months: Unknown///characteristics_ch2.8: disease status: Unknown///characteristics_ch2.9: patient status: Unknown///characteristics_ch2.10: disease state: Malignant ovarian///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238160/GSM1238160_US22502615_251209747447_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-017///geo_accession: GSM1238161///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-017///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 10///characteristics_ch2.3: age at surgery: 60.85///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1031///characteristics_ch2.9: follow up months: 19///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Dead///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238161/GSM1238161_US22502615_251209750982_S02_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-018///geo_accession: GSM1238162///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-018///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.8///characteristics_ch2.3: age at surgery: 43.81///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1028///characteristics_ch2.9: follow up months: 55///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Dead///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238162/GSM1238162_US22502615_251209747422_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-019///geo_accession: GSM1238163///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-019///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.1///characteristics_ch2.3: age at surgery: 45.53///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 26///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238163/GSM1238163_US22502615_251209747425_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-020///geo_accession: GSM1238164///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-020///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.6///characteristics_ch2.3: age at surgery: 37.07///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IC///characteristics_ch2.6: grade: unknown///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 68///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238164/GSM1238164_US22502615_251209749022_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-021///geo_accession: GSM1238165///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-021///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 7.8///characteristics_ch2.3: age at surgery: 80.24///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIB///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 73///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238165/GSM1238165_US22502615_251209749840_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-022///geo_accession: GSM1238166///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-022///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.1///characteristics_ch2.3: age at surgery: 65.60///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 76///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238166/GSM1238166_US22502615_251209749644_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-023///geo_accession: GSM1238167///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-023///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.7///characteristics_ch2.3: age at surgery: 45.98///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 57///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238167/GSM1238167_US22502615_251209750936_S02_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-024///geo_accession: GSM1238168///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-024///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 62.98///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1109///characteristics_ch2.9: follow up months: 51///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Dead///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238168/GSM1238168_US22502615_251209754217_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-025///geo_accession: GSM1238169///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-025///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.9///characteristics_ch2.3: age at surgery: 52.79///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 11///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238169/GSM1238169_US22502615_251209750984_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-026///geo_accession: GSM1238170///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-026///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.5///characteristics_ch2.3: age at surgery: 52.25///characteristics_ch2.4: histology: Normal///characteristics_ch2.5: tissue status: Benign///characteristics_ch2.6: disease status: Benign///characteristics_ch2.7: patient status: Benign///characteristics_ch2.8: disease state: Normal ovarian///characteristics_ch2.9: ///characteristics_ch2.10: ///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Normal_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238170/GSM1238170_US22502615_251209747043_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-027///geo_accession: GSM1238171///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-027///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.1///characteristics_ch2.3: age at surgery: 56.86///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 49///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238171/GSM1238171_US22502615_251209749047_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-028///geo_accession: GSM1238172///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-028///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 26.44///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 0///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 59///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238172/GSM1238172_US22502615_251209749774_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-029///geo_accession: GSM1238173///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-029///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 55.66///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 18///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238173/GSM1238173_US22502615_251209750969_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-030///geo_accession: GSM1238174///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-030///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.7///characteristics_ch2.3: age at surgery: 60.03///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 11///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238174/GSM1238174_US22502615_251209754146_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-031///geo_accession: GSM1238175///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-031///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: age at surgery: 45.32///characteristics_ch2.3: histology: Serous///characteristics_ch2.4: Stage: IV///characteristics_ch2.5: grade: 3///characteristics_ch2.6: tissue status: Primary///characteristics_ch2.7: tcga id: TCGA-23-2077///characteristics_ch2.8: follow up months: 120///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238175/GSM1238175_US22502615_251209750933_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-032///geo_accession: GSM1238176///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-032///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 60.71///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 49///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238176/GSM1238176_US22502615_251209754797_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-033///geo_accession: GSM1238177///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-033///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.2///characteristics_ch2.3: age at surgery: 55.26///characteristics_ch2.4: histology: Normal///characteristics_ch2.5: tissue status: Benign///characteristics_ch2.6: disease status: Benign///characteristics_ch2.7: patient status: Benign///characteristics_ch2.8: disease state: Normal ovarian///characteristics_ch2.9: ///characteristics_ch2.10: ///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Normal_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238177/GSM1238177_US22502615_251209749469_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-034///geo_accession: GSM1238178///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-034///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.6///characteristics_ch2.3: age at surgery: 34.28///characteristics_ch2.4: histology: Mucinous///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 210///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238178/GSM1238178_US22502615_251209754210_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-035///geo_accession: GSM1238179///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-035///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 74.26///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIA///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 37///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238179/GSM1238179_US22502615_251209747091_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-036///geo_accession: GSM1238180///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-036///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 47.47///characteristics_ch2.4: histology: Mucinous///characteristics_ch2.5: Stage: IC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 176///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238180/GSM1238180_US22502615_251209749642_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-037///geo_accession: GSM1238181///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-037///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.6///characteristics_ch2.3: age at surgery: 78.02///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 39///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238181/GSM1238181_US22502615_251209754165_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-038///geo_accession: GSM1238182///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-038///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 80.72///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 17///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238182/GSM1238182_US22502615_251209754214_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-039///geo_accession: GSM1238183///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-039///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8///characteristics_ch2.3: age at surgery: 52.40///characteristics_ch2.4: histology: Endometrioid///characteristics_ch2.5: Stage: IC///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 209///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238183/GSM1238183_US22502615_251209754164_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-040///geo_accession: GSM1238184///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-040///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.5///characteristics_ch2.3: age at surgery: 61.69///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIB///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 31///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238184/GSM1238184_US22502615_251209750938_S02_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-041///geo_accession: GSM1238185///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-041///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.3///characteristics_ch2.3: age at surgery: 73.50///characteristics_ch2.4: histology: Normal///characteristics_ch2.5: tissue status: Benign///characteristics_ch2.6: disease status: Benign///characteristics_ch2.7: patient status: Benign///characteristics_ch2.8: disease state: Normal ovarian///characteristics_ch2.9: ///characteristics_ch2.10: ///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Normal_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238185/GSM1238185_US22502615_251209747511_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-042///geo_accession: GSM1238186///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-042///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.1///characteristics_ch2.3: age at surgery: 45.10///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1118///characteristics_ch2.9: follow up months: 113///characteristics_ch2.10: disease status: Free///characteristics_ch2.11: patient status: Alive///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238186/GSM1238186_US22502615_251209747044_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-043///geo_accession: GSM1238187///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-043///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.8///characteristics_ch2.3: age at surgery: 55.27///characteristics_ch2.4: histology: Normal///characteristics_ch2.5: tissue status: Benign///characteristics_ch2.6: disease status: Benign///characteristics_ch2.7: patient status: Benign///characteristics_ch2.8: disease state: Normal ovarian///characteristics_ch2.9: ///characteristics_ch2.10: ///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Normal_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238187/GSM1238187_US22502615_251209750940_S02_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-044///geo_accession: GSM1238188///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-044///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.5///characteristics_ch2.3: age at surgery: 43.37///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 26///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238188/GSM1238188_US22502615_251209754234_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-045///geo_accession: GSM1238189///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-045///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.6///characteristics_ch2.3: age at surgery: 72.37///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 14///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238189/GSM1238189_US22502615_251209749468_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-046///geo_accession: GSM1238190///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-046///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 67.44///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 2///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238190/GSM1238190_US22502615_251209749773_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-047///geo_accession: GSM1238191///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-047///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.6///characteristics_ch2.3: age at surgery: 54.39///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 0///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 80///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238191/GSM1238191_US22502615_251209749048_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-048///geo_accession: GSM1238192///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-048///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 10///characteristics_ch2.3: age at surgery: 39.97///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 90///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238192/GSM1238192_US22502615_251209754157_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-049///geo_accession: GSM1238193///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-049///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.5///characteristics_ch2.3: age at surgery: 80.67///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 18///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238193/GSM1238193_US22502615_251209747538_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-050///geo_accession: GSM1238194///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-050///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9///characteristics_ch2.3: age at surgery: 75.58///characteristics_ch2.4: histology: Endometrioid///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 58///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238194/GSM1238194_US22502615_251209754775_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-051///geo_accession: GSM1238195///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-051///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.7///characteristics_ch2.3: age at surgery: 57.98///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 29///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238195/GSM1238195_US22502615_251209747187_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-052///geo_accession: GSM1238196///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-052///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.2///characteristics_ch2.3: age at surgery: 41.63///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 8///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238196/GSM1238196_US22502615_251209750951_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-053///geo_accession: GSM1238197///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-053///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 10///characteristics_ch2.3: age at surgery: 63.56///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 11///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238197/GSM1238197_US22502615_251209754150_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-054///geo_accession: GSM1238198///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-054///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 7.4///characteristics_ch2.3: age at surgery: 54.26///characteristics_ch2.4: histology: Mucinous///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 0///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 72///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238198/GSM1238198_US22502615_251209747550_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-055///geo_accession: GSM1238199///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-055///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.8///characteristics_ch2.3: age at surgery: 66.46///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 152///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238199/GSM1238199_US22502615_251209754168_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-056///geo_accession: GSM1238200///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-056///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.8///characteristics_ch2.3: age at surgery: 57.97///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 15///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238200/GSM1238200_US22502615_251209748613_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-057///geo_accession: GSM1238201///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-057///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 53.07///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIA///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 205///characteristics_ch2.9: disease status: Unknown///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238201/GSM1238201_US22502615_251209750953_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-058///geo_accession: GSM1238202///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-058///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 83.07///characteristics_ch2.4: histology: MMMT///characteristics_ch2.5: Stage: IC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 1///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238202/GSM1238202_US22502615_251209751001_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-059///geo_accession: GSM1238203///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-059///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 42.17///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 16///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238203/GSM1238203_US22502615_251209751002_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-060///geo_accession: GSM1238204///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-060///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.6///characteristics_ch2.3: age at surgery: 51.58///characteristics_ch2.4: histology: Endometrioid///characteristics_ch2.5: Stage: IIIB///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 56///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238204/GSM1238204_US22502615_251209754144_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-061///geo_accession: GSM1238205///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-061///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 10///characteristics_ch2.3: age at surgery: 30.32///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 1///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 90///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238205/GSM1238205_US22502615_251209750996_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-062///geo_accession: GSM1238206///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-062///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.9///characteristics_ch2.3: age at surgery: 48.71///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1113///characteristics_ch2.9: follow up months: 31///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Dead///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238206/GSM1238206_US22502615_251209750995_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-063///geo_accession: GSM1238207///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-063///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.6///characteristics_ch2.3: age at surgery: 59.96///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 47///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238207/GSM1238207_US22502615_251209749839_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-064///geo_accession: GSM1238208///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-064///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.1///characteristics_ch2.3: age at surgery: 54.02///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC/IA///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 64///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238208/GSM1238208_US22502615_251209754725_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-065///geo_accession: GSM1238209///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-065///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.9///characteristics_ch2.3: age at surgery: 45.16///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-2084///characteristics_ch2.9: follow up months: 50///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Dead///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238209/GSM1238209_US22502615_251209754133_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-066///geo_accession: GSM1238210///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-066///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.2///characteristics_ch2.3: age at surgery: 83.94///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IB///characteristics_ch2.6: grade: unknown///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 159///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238210/GSM1238210_US22502615_251209749643_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-067///geo_accession: GSM1238211///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-067///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 7.2///characteristics_ch2.3: age at surgery: 67.48///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IB///characteristics_ch2.6: grade: 1///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 74///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238211/GSM1238211_US22502615_251209754132_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-068///geo_accession: GSM1238212///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-068///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 63.58///characteristics_ch2.4: histology: Benign///characteristics_ch2.5: tissue status: Benign///characteristics_ch2.6: follow up months: 87///characteristics_ch2.7: disease status: Free///characteristics_ch2.8: patient status: Alive///characteristics_ch2.9: disease state: Benign ovarian///characteristics_ch2.10: ///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Benign_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238212/GSM1238212_US22502615_251209754111_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-069///geo_accession: GSM1238213///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-069///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.1///characteristics_ch2.3: age at surgery: 57.43///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 101///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238213/GSM1238213_US22502615_251209749502_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-070///geo_accession: GSM1238214///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-070///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.9///characteristics_ch2.3: age at surgery: 80.93///characteristics_ch2.4: histology: Clear Cell///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 96///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238214/GSM1238214_US22502615_251209751009_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-071///geo_accession: GSM1238215///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-071///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 28.39///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 43///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238215/GSM1238215_US22502615_251209747450_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-072///geo_accession: GSM1238216///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-072///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.7///characteristics_ch2.3: age at surgery: 73.52///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIB///characteristics_ch2.6: grade: 1///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 36///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238216/GSM1238216_US22502615_251209754724_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-073///geo_accession: GSM1238217///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-073///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 65.23///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1023///characteristics_ch2.9: follow up months: 67///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Alive///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238217/GSM1238217_US22502615_251209754782_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-074///geo_accession: GSM1238218///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-074///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9///characteristics_ch2.3: age at surgery: 45.61///characteristics_ch2.4: histology: Benign///characteristics_ch2.5: tissue status: Benign///characteristics_ch2.6: disease status: Benign///characteristics_ch2.7: patient status: Benign///characteristics_ch2.8: disease state: Benign ovarian///characteristics_ch2.9: ///characteristics_ch2.10: ///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Benign_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238218/GSM1238218_US22502615_251209747078_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-075///geo_accession: GSM1238219///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-075///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 72.21///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IC///characteristics_ch2.6: grade: 0///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 98///characteristics_ch2.9: disease status: Unknown///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238219/GSM1238219_US22502615_251209754148_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-076///geo_accession: GSM1238220///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-076///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8///characteristics_ch2.3: age at surgery: 67.35///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 37///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238220/GSM1238220_US22502615_251209754237_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-077///geo_accession: GSM1238221///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-077///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 48.15///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1027///characteristics_ch2.9: follow up months: 32///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Dead///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238221/GSM1238221_US22502615_251209754776_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-078///geo_accession: GSM1238222///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-078///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9///characteristics_ch2.3: age at surgery: 68.88///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 12///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238222/GSM1238222_US22502615_251209747449_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-079///geo_accession: GSM1238223///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-079///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.2///characteristics_ch2.3: age at surgery: 63.50///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 27///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238223/GSM1238223_US22502615_251209754155_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-080///geo_accession: GSM1238224///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-080///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 8.3///characteristics_ch2.3: age at surgery: 67.53///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 25///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238224/GSM1238224_US22502615_251209747092_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-081///geo_accession: GSM1238225///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-081///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.8///characteristics_ch2.3: age at surgery: 55.90///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 32///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238225/GSM1238225_US22502615_251209749836_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-082///geo_accession: GSM1238226///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-082///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 52.05///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 36///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238226/GSM1238226_US22502615_251209750955_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-083///geo_accession: GSM1238227///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-083///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.5///characteristics_ch2.3: age at surgery: 85.52///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 14///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238227/GSM1238227_US22502615_251209754808_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-084///geo_accession: GSM1238228///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-084///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 51.36///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 210///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238228/GSM1238228_US22502615_251209749355_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-085///geo_accession: GSM1238229///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-085///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 56.74///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 50///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238229/GSM1238229_US22502615_251209754088_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-086///geo_accession: GSM1238230///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-086///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.6///characteristics_ch2.3: age at surgery: 75.01///characteristics_ch2.4: histology: Endometrioid///characteristics_ch2.5: Stage: IIC///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 67///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238230/GSM1238230_US22502615_251209754135_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-087///geo_accession: GSM1238231///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-087///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.3///characteristics_ch2.3: age at surgery: 62.84///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC/IB///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 51///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238231/GSM1238231_US22502615_251209754787_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-088///geo_accession: GSM1238232///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-088///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 45.02///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIB///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1026///characteristics_ch2.9: follow up months: 50///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Alive///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238232/GSM1238232_US22502615_251209754151_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-089///geo_accession: GSM1238233///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-089///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.9///characteristics_ch2.3: age at surgery: 42.79///characteristics_ch2.4: histology: Mucinous///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 0///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 79///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238233/GSM1238233_US22502615_251209749024_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-090///geo_accession: GSM1238234///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-090///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 64.32///characteristics_ch2.4: histology: Endometrioid///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 211///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238234/GSM1238234_US22502615_251209754235_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-091///geo_accession: GSM1238235///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-091///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 10///characteristics_ch2.3: age at surgery: 64.85///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1119///characteristics_ch2.9: follow up months: 140///characteristics_ch2.10: disease status: Free///characteristics_ch2.11: patient status: Alive///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238235/GSM1238235_US22502615_251209750935_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-092///geo_accession: GSM1238236///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-092///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.6///characteristics_ch2.3: age at surgery: 44.53///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIA///characteristics_ch2.6: grade: 1///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 34///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238236/GSM1238236_US22502615_251209754798_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-093///geo_accession: GSM1238237///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-093///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 53.49///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1102///characteristics_ch2.9: follow up months: 39///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Dead///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238237/GSM1238237_US22502615_251209747093_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-094///geo_accession: GSM1238238///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-094///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.4///characteristics_ch2.3: age at surgery: 63.21///characteristics_ch2.4: histology: Transitional Cell///characteristics_ch2.5: Stage: IIA///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 77///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238238/GSM1238238_US22502615_251209754213_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-095///geo_accession: GSM1238239///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-095///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 68.12///characteristics_ch2.4: histology: Mucinous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 24///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238239/GSM1238239_US22502615_251209754154_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-096///geo_accession: GSM1238240///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-096///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 10///characteristics_ch2.3: age at surgery: 66.32///characteristics_ch2.4: histology: Endometrioid///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 1///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 57///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238240/GSM1238240_US22502615_251209747077_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-097///geo_accession: GSM1238241///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-097///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 64.44///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 19///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238241/GSM1238241_US22502615_251209754166_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-098///geo_accession: GSM1238242///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-098///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.1///characteristics_ch2.3: age at surgery: 73.61///characteristics_ch2.4: histology: MMMT///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 17///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238242/GSM1238242_US22502615_251209754147_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-099///geo_accession: GSM1238243///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-099///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.7///characteristics_ch2.3: age at surgery: 68.22///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 14///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238243/GSM1238243_US22502615_251209749771_S01_A01.txt.gz///data_row_count: 20173
1
(Other)
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Value
An expression set
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Description Format Details Value
Description
To identify molecular prognosticators and therapeutic targets for high-grade serous epithelial ovarian cancers (EOCs) using genetic analyses driven by biologic features of EOC pathogenesis.Ovarian tissue samples (n = 172; 122 serous EOCs, 30 other EOCs, 20 normal/benign) collected prospectively from sequential patients undergoing gynecologic surgery were analyzed using RNA expression microarrays. Samples were classified based on expression of genes with potential relevance in ovarian cancer. Gene sets were defined using Rosetta Similarity Search Tool (ROAST) and analysis of variance (ANOVA). Gene copy number variations were identified by array comparative genomic hybridization.No distinct subgroups of EOC could be identified by unsupervised clustering, however, analyses based on genes correlated with periostin (POSTN) and estrogen receptor-alpha (ESR1) yielded distinct subgroups. When 95 high-grade serous EOCs were grouped by genes based on ANOVA comparing ESR1/WT1 and POSTN/TGFBI samples, overall survival (OS) was significantly shorter for 43 patients with tumors expressing genes associated with POSTN/TGFBI compared to 52 patients with tumors expressing genes associated with ESR1/WT1 (median 30 versus 49 months, respectively; P = 0.022). Several targets with therapeutic potential were identified within each subgroup. BRCA germline mutations were more frequent in the ESR1/WT1 subgroup. Proliferation-associated genes and TP53 status (mutated or wild-type) did not correlate with survival. Findings were validated using independent ovarian cancer datasets.Two distinct molecular subgroups of high-grade serous EOCs based on POSTN/TGFBI and ESR1/WT1 expressions were identified with significantly different OS. Specific differentially expressed genes between these subgroups provide potential prognostic and therapeutic targets.Copyright ?? 2013 Elsevier Inc. All rights reserved.
Format
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | experimentData(eset):
Experiment data
Experimenter name: Karlan BY, Dering J, Walsh C, Orsulic S, Lester J, Anderson LA, Ginther CL, Fejzo M, Slamon D
Laboratory: Karlan, Slamon 2014
Contact information:
Title: POSTN/TGFBI-associated stromal signature predicts poor prognosis in serous epithelial ovarian cancer.
URL:
PMIDs: 24368280
Abstract: A 250 word abstract is available. Use 'abstract' method.
Information is available on: preprocessing
notes:
platform_title:
Agilent-012097 Human 1A Microarray (V2) G4110B (Probe Name version)
platform_shorttitle:
Agilent G4110B
platform_summary:
hgug4110b
platform_manufacturer:
Agilent
platform_distribution:
commercial
platform_accession:
GPL7264
platform_technology:
in situ oligonucleotide
version:
2015-09-22 20:05:48
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: A_23_P100001 A_23_P100011 ... A_23_P99996 (18703 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
|
Details
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 | assayData: 18703 features, 172 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
20 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
152.00 112.00 4.13 3.50 4.92
---------------------------
Available sample meta-data:
---------------------------
alt_sample_name:
Ov_Tumor_Ref_Mix vs. CS-OV-001 Ov_Tumor_Ref_Mix vs. CS-OV-002
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-003 Ov_Tumor_Ref_Mix vs. CS-OV-004
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-005 Ov_Tumor_Ref_Mix vs. CS-OV-006
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-007 Ov_Tumor_Ref_Mix vs. CS-OV-008
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-009 Ov_Tumor_Ref_Mix vs. CS-OV-010
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-011 Ov_Tumor_Ref_Mix vs. CS-OV-012
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-013 Ov_Tumor_Ref_Mix vs. CS-OV-014
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-015 Ov_Tumor_Ref_Mix vs. CS-OV-016
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-017 Ov_Tumor_Ref_Mix vs. CS-OV-018
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-019 Ov_Tumor_Ref_Mix vs. CS-OV-020
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-021 Ov_Tumor_Ref_Mix vs. CS-OV-022
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-023 Ov_Tumor_Ref_Mix vs. CS-OV-024
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-025 Ov_Tumor_Ref_Mix vs. CS-OV-026
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-027 Ov_Tumor_Ref_Mix vs. CS-OV-028
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-029 Ov_Tumor_Ref_Mix vs. CS-OV-030
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-031 Ov_Tumor_Ref_Mix vs. CS-OV-032
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-033 Ov_Tumor_Ref_Mix vs. CS-OV-034
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-035 Ov_Tumor_Ref_Mix vs. CS-OV-036
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-037 Ov_Tumor_Ref_Mix vs. CS-OV-038
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-039 Ov_Tumor_Ref_Mix vs. CS-OV-040
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-041 Ov_Tumor_Ref_Mix vs. CS-OV-042
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-043 Ov_Tumor_Ref_Mix vs. CS-OV-044
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-045 Ov_Tumor_Ref_Mix vs. CS-OV-046
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-047 Ov_Tumor_Ref_Mix vs. CS-OV-048
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-049 Ov_Tumor_Ref_Mix vs. CS-OV-050
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-051 Ov_Tumor_Ref_Mix vs. CS-OV-052
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-053 Ov_Tumor_Ref_Mix vs. CS-OV-054
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-055 Ov_Tumor_Ref_Mix vs. CS-OV-056
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-057 Ov_Tumor_Ref_Mix vs. CS-OV-058
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-059 Ov_Tumor_Ref_Mix vs. CS-OV-060
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-061 Ov_Tumor_Ref_Mix vs. CS-OV-062
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-063 Ov_Tumor_Ref_Mix vs. CS-OV-064
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-065 Ov_Tumor_Ref_Mix vs. CS-OV-066
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-067 Ov_Tumor_Ref_Mix vs. CS-OV-068
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-069 Ov_Tumor_Ref_Mix vs. CS-OV-070
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-071 Ov_Tumor_Ref_Mix vs. CS-OV-072
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-073 Ov_Tumor_Ref_Mix vs. CS-OV-074
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-075 Ov_Tumor_Ref_Mix vs. CS-OV-076
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-077 Ov_Tumor_Ref_Mix vs. CS-OV-078
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-079 Ov_Tumor_Ref_Mix vs. CS-OV-080
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-081 Ov_Tumor_Ref_Mix vs. CS-OV-082
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-083 Ov_Tumor_Ref_Mix vs. CS-OV-084
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-085 Ov_Tumor_Ref_Mix vs. CS-OV-086
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-087 Ov_Tumor_Ref_Mix vs. CS-OV-088
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-089 Ov_Tumor_Ref_Mix vs. CS-OV-090
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-091 Ov_Tumor_Ref_Mix vs. CS-OV-092
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-093 Ov_Tumor_Ref_Mix vs. CS-OV-094
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-095 Ov_Tumor_Ref_Mix vs. CS-OV-096
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-097 Ov_Tumor_Ref_Mix vs. CS-OV-098
1 1
Ov_Tumor_Ref_Mix vs. CS-OV-099 (Other)
1 73
sample_type:
benign borderline healthy metastatic tumor
5 12 15 17 123
histological_type:
clearcell endo mucinous other ser NA's
3 7 9 11 122 20
summarygrade:
high low NA's
119 30 23
summarystage:
early late NA's
31 120 21
tumorstage:
1 2 3 4 NA's
22 9 103 17 21
substage:
a b c NA's
17 22 94 39
grade:
0 1 2 3 NA's
8 8 14 119 23
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
26.0 49.0 57.5 58.6 68.0 91.0
neo:
n
172
recurrence_status:
norecurrence recurrence NA's
36 111 25
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30 791 1491 1835 2344 7001 20
vital_status:
deceased living NA's
112 40 20
percent_normal_cells:
30- NA's
140 32
percent_stromal_cells:
30- NA's
140 32
percent_tumor_cells:
70+ NA's
140 32
uncurated_author_metadata:
title: Ov_Tumor_Ref_Mix vs. CS-OV-001///geo_accession: GSM1238145///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-001///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.8///characteristics_ch2.3: age at surgery: 50.45///characteristics_ch2.4: histology: MMMT///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 7///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238145/GSM1238145_US22502615_251209750932_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-002///geo_accession: GSM1238146///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-002///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.5///characteristics_ch2.3: age at surgery: 75.69///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 26///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238146/GSM1238146_US22502615_251209754104_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-003///geo_accession: GSM1238147///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-003///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 39.66///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 1///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 103///characteristics_ch2.9: disease status: Unknown///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238147/GSM1238147_US22502615_251209750994_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-004///geo_accession: GSM1238148///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-004///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.2///characteristics_ch2.3: age at surgery: 69.33///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 33///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238148/GSM1238148_US22502615_251209747186_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-005///geo_accession: GSM1238149///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-005///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.5///characteristics_ch2.3: age at surgery: 82.01///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIB///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 54///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238149/GSM1238149_US22502615_251209749503_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-006///geo_accession: GSM1238150///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-006///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 7.5///characteristics_ch2.3: age at surgery: 58.56///characteristics_ch2.4: histology: Adenocarcinoma///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 41///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238150/GSM1238150_US22502615_251209747514_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-007///geo_accession: GSM1238151///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-007///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.3///characteristics_ch2.3: age at surgery: 69.32///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIB///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 6///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238151/GSM1238151_US22502615_251209754110_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-008///geo_accession: GSM1238152///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-008///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 63.54///characteristics_ch2.4: histology: MMMT///characteristics_ch2.5: Stage: IIB///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 9///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238152/GSM1238152_US22502615_251209750954_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-009///geo_accession: GSM1238153///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-009///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.2///characteristics_ch2.3: age at surgery: 67.91///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 22///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238153/GSM1238153_US22502615_251209754145_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-010///geo_accession: GSM1238154///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-010///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 85.58///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 9///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238154/GSM1238154_US22502615_251209749837_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-011///geo_accession: GSM1238155///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-011///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 39.50///characteristics_ch2.4: histology: Mucinous///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 0///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 67///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238155/GSM1238155_US22502615_251209754811_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-012///geo_accession: GSM1238156///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-012///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 7.9///characteristics_ch2.3: age at surgery: 68.16///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 42///characteristics_ch2.9: disease status: Unknown///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238156/GSM1238156_US22502615_251209754098_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-013///geo_accession: GSM1238157///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-013///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.9///characteristics_ch2.3: age at surgery: 44.95///characteristics_ch2.4: histology: Normal///characteristics_ch2.5: tissue status: Benign///characteristics_ch2.6: disease status: Benign///characteristics_ch2.7: patient status: Benign///characteristics_ch2.8: disease state: Normal ovarian///characteristics_ch2.9: ///characteristics_ch2.10: ///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Normal_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238157/GSM1238157_US22502615_251209747185_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-014///geo_accession: GSM1238158///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-014///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9///characteristics_ch2.3: age at surgery: 59.66///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 66///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238158/GSM1238158_US22502615_251209751008_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-015///geo_accession: GSM1238159///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-015///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.2///characteristics_ch2.3: age at surgery: 62.28///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 73///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238159/GSM1238159_US22502615_251209754814_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-016///geo_accession: GSM1238160///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-016///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.2///characteristics_ch2.3: age at surgery: 90.78///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: grade: unknown///characteristics_ch2.6: tissue status: Primary///characteristics_ch2.7: follow up months: Unknown///characteristics_ch2.8: disease status: Unknown///characteristics_ch2.9: patient status: Unknown///characteristics_ch2.10: disease state: Malignant ovarian///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238160/GSM1238160_US22502615_251209747447_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-017///geo_accession: GSM1238161///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-017///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 10///characteristics_ch2.3: age at surgery: 60.85///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1031///characteristics_ch2.9: follow up months: 19///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Dead///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238161/GSM1238161_US22502615_251209750982_S02_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-018///geo_accession: GSM1238162///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-018///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.8///characteristics_ch2.3: age at surgery: 43.81///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1028///characteristics_ch2.9: follow up months: 55///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Dead///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238162/GSM1238162_US22502615_251209747422_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-019///geo_accession: GSM1238163///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-019///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.1///characteristics_ch2.3: age at surgery: 45.53///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 26///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238163/GSM1238163_US22502615_251209747425_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-020///geo_accession: GSM1238164///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-020///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.6///characteristics_ch2.3: age at surgery: 37.07///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IC///characteristics_ch2.6: grade: unknown///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 68///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238164/GSM1238164_US22502615_251209749022_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-021///geo_accession: GSM1238165///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-021///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 7.8///characteristics_ch2.3: age at surgery: 80.24///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIB///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 73///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238165/GSM1238165_US22502615_251209749840_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-022///geo_accession: GSM1238166///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-022///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.1///characteristics_ch2.3: age at surgery: 65.60///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 76///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238166/GSM1238166_US22502615_251209749644_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-023///geo_accession: GSM1238167///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-023///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.7///characteristics_ch2.3: age at surgery: 45.98///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 57///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238167/GSM1238167_US22502615_251209750936_S02_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-024///geo_accession: GSM1238168///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-024///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 62.98///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1109///characteristics_ch2.9: follow up months: 51///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Dead///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238168/GSM1238168_US22502615_251209754217_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-025///geo_accession: GSM1238169///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-025///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.9///characteristics_ch2.3: age at surgery: 52.79///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 11///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238169/GSM1238169_US22502615_251209750984_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-026///geo_accession: GSM1238170///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-026///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.5///characteristics_ch2.3: age at surgery: 52.25///characteristics_ch2.4: histology: Normal///characteristics_ch2.5: tissue status: Benign///characteristics_ch2.6: disease status: Benign///characteristics_ch2.7: patient status: Benign///characteristics_ch2.8: disease state: Normal ovarian///characteristics_ch2.9: ///characteristics_ch2.10: ///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Normal_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238170/GSM1238170_US22502615_251209747043_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-027///geo_accession: GSM1238171///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-027///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.1///characteristics_ch2.3: age at surgery: 56.86///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 49///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238171/GSM1238171_US22502615_251209749047_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-028///geo_accession: GSM1238172///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-028///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 26.44///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 0///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 59///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238172/GSM1238172_US22502615_251209749774_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-029///geo_accession: GSM1238173///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-029///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 55.66///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 18///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238173/GSM1238173_US22502615_251209750969_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-030///geo_accession: GSM1238174///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-030///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.7///characteristics_ch2.3: age at surgery: 60.03///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 11///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238174/GSM1238174_US22502615_251209754146_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-031///geo_accession: GSM1238175///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-031///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: age at surgery: 45.32///characteristics_ch2.3: histology: Serous///characteristics_ch2.4: Stage: IV///characteristics_ch2.5: grade: 3///characteristics_ch2.6: tissue status: Primary///characteristics_ch2.7: tcga id: TCGA-23-2077///characteristics_ch2.8: follow up months: 120///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238175/GSM1238175_US22502615_251209750933_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-032///geo_accession: GSM1238176///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-032///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 60.71///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 49///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238176/GSM1238176_US22502615_251209754797_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-033///geo_accession: GSM1238177///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-033///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.2///characteristics_ch2.3: age at surgery: 55.26///characteristics_ch2.4: histology: Normal///characteristics_ch2.5: tissue status: Benign///characteristics_ch2.6: disease status: Benign///characteristics_ch2.7: patient status: Benign///characteristics_ch2.8: disease state: Normal ovarian///characteristics_ch2.9: ///characteristics_ch2.10: ///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Normal_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238177/GSM1238177_US22502615_251209749469_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-034///geo_accession: GSM1238178///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-034///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.6///characteristics_ch2.3: age at surgery: 34.28///characteristics_ch2.4: histology: Mucinous///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 210///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238178/GSM1238178_US22502615_251209754210_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-035///geo_accession: GSM1238179///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-035///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 74.26///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIA///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 37///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238179/GSM1238179_US22502615_251209747091_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-036///geo_accession: GSM1238180///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-036///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 47.47///characteristics_ch2.4: histology: Mucinous///characteristics_ch2.5: Stage: IC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 176///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238180/GSM1238180_US22502615_251209749642_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-037///geo_accession: GSM1238181///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-037///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.6///characteristics_ch2.3: age at surgery: 78.02///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 39///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238181/GSM1238181_US22502615_251209754165_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-038///geo_accession: GSM1238182///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-038///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 80.72///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 17///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238182/GSM1238182_US22502615_251209754214_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-039///geo_accession: GSM1238183///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-039///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8///characteristics_ch2.3: age at surgery: 52.40///characteristics_ch2.4: histology: Endometrioid///characteristics_ch2.5: Stage: IC///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 209///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238183/GSM1238183_US22502615_251209754164_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-040///geo_accession: GSM1238184///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-040///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.5///characteristics_ch2.3: age at surgery: 61.69///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIB///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 31///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238184/GSM1238184_US22502615_251209750938_S02_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-041///geo_accession: GSM1238185///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-041///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.3///characteristics_ch2.3: age at surgery: 73.50///characteristics_ch2.4: histology: Normal///characteristics_ch2.5: tissue status: Benign///characteristics_ch2.6: disease status: Benign///characteristics_ch2.7: patient status: Benign///characteristics_ch2.8: disease state: Normal ovarian///characteristics_ch2.9: ///characteristics_ch2.10: ///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Normal_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238185/GSM1238185_US22502615_251209747511_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-042///geo_accession: GSM1238186///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-042///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.1///characteristics_ch2.3: age at surgery: 45.10///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1118///characteristics_ch2.9: follow up months: 113///characteristics_ch2.10: disease status: Free///characteristics_ch2.11: patient status: Alive///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238186/GSM1238186_US22502615_251209747044_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-043///geo_accession: GSM1238187///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-043///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.8///characteristics_ch2.3: age at surgery: 55.27///characteristics_ch2.4: histology: Normal///characteristics_ch2.5: tissue status: Benign///characteristics_ch2.6: disease status: Benign///characteristics_ch2.7: patient status: Benign///characteristics_ch2.8: disease state: Normal ovarian///characteristics_ch2.9: ///characteristics_ch2.10: ///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Normal_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238187/GSM1238187_US22502615_251209750940_S02_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-044///geo_accession: GSM1238188///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-044///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.5///characteristics_ch2.3: age at surgery: 43.37///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 26///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238188/GSM1238188_US22502615_251209754234_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-045///geo_accession: GSM1238189///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-045///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.6///characteristics_ch2.3: age at surgery: 72.37///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 14///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238189/GSM1238189_US22502615_251209749468_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-046///geo_accession: GSM1238190///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-046///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 67.44///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 2///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238190/GSM1238190_US22502615_251209749773_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-047///geo_accession: GSM1238191///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-047///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.6///characteristics_ch2.3: age at surgery: 54.39///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 0///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 80///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238191/GSM1238191_US22502615_251209749048_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-048///geo_accession: GSM1238192///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-048///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 10///characteristics_ch2.3: age at surgery: 39.97///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 90///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238192/GSM1238192_US22502615_251209754157_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-049///geo_accession: GSM1238193///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-049///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.5///characteristics_ch2.3: age at surgery: 80.67///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 18///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238193/GSM1238193_US22502615_251209747538_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-050///geo_accession: GSM1238194///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-050///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9///characteristics_ch2.3: age at surgery: 75.58///characteristics_ch2.4: histology: Endometrioid///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 58///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238194/GSM1238194_US22502615_251209754775_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-051///geo_accession: GSM1238195///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-051///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.7///characteristics_ch2.3: age at surgery: 57.98///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 29///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238195/GSM1238195_US22502615_251209747187_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-052///geo_accession: GSM1238196///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-052///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.2///characteristics_ch2.3: age at surgery: 41.63///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 8///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238196/GSM1238196_US22502615_251209750951_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-053///geo_accession: GSM1238197///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-053///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 10///characteristics_ch2.3: age at surgery: 63.56///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 11///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238197/GSM1238197_US22502615_251209754150_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-054///geo_accession: GSM1238198///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-054///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 7.4///characteristics_ch2.3: age at surgery: 54.26///characteristics_ch2.4: histology: Mucinous///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 0///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 72///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238198/GSM1238198_US22502615_251209747550_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-055///geo_accession: GSM1238199///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-055///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.8///characteristics_ch2.3: age at surgery: 66.46///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 152///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238199/GSM1238199_US22502615_251209754168_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-056///geo_accession: GSM1238200///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-056///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.8///characteristics_ch2.3: age at surgery: 57.97///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 15///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238200/GSM1238200_US22502615_251209748613_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-057///geo_accession: GSM1238201///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-057///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 53.07///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIA///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 205///characteristics_ch2.9: disease status: Unknown///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238201/GSM1238201_US22502615_251209750953_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-058///geo_accession: GSM1238202///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-058///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 83.07///characteristics_ch2.4: histology: MMMT///characteristics_ch2.5: Stage: IC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 1///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238202/GSM1238202_US22502615_251209751001_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-059///geo_accession: GSM1238203///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-059///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 42.17///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 16///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238203/GSM1238203_US22502615_251209751002_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-060///geo_accession: GSM1238204///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-060///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.6///characteristics_ch2.3: age at surgery: 51.58///characteristics_ch2.4: histology: Endometrioid///characteristics_ch2.5: Stage: IIIB///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 56///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238204/GSM1238204_US22502615_251209754144_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-061///geo_accession: GSM1238205///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-061///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 10///characteristics_ch2.3: age at surgery: 30.32///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 1///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 90///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238205/GSM1238205_US22502615_251209750996_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-062///geo_accession: GSM1238206///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-062///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.9///characteristics_ch2.3: age at surgery: 48.71///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1113///characteristics_ch2.9: follow up months: 31///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Dead///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238206/GSM1238206_US22502615_251209750995_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-063///geo_accession: GSM1238207///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-063///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.6///characteristics_ch2.3: age at surgery: 59.96///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 47///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238207/GSM1238207_US22502615_251209749839_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-064///geo_accession: GSM1238208///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-064///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.1///characteristics_ch2.3: age at surgery: 54.02///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC/IA///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 64///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238208/GSM1238208_US22502615_251209754725_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-065///geo_accession: GSM1238209///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-065///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.9///characteristics_ch2.3: age at surgery: 45.16///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-2084///characteristics_ch2.9: follow up months: 50///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Dead///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238209/GSM1238209_US22502615_251209754133_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-066///geo_accession: GSM1238210///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-066///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.2///characteristics_ch2.3: age at surgery: 83.94///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IB///characteristics_ch2.6: grade: unknown///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 159///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238210/GSM1238210_US22502615_251209749643_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-067///geo_accession: GSM1238211///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-067///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 7.2///characteristics_ch2.3: age at surgery: 67.48///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IB///characteristics_ch2.6: grade: 1///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 74///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238211/GSM1238211_US22502615_251209754132_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-068///geo_accession: GSM1238212///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-068///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 63.58///characteristics_ch2.4: histology: Benign///characteristics_ch2.5: tissue status: Benign///characteristics_ch2.6: follow up months: 87///characteristics_ch2.7: disease status: Free///characteristics_ch2.8: patient status: Alive///characteristics_ch2.9: disease state: Benign ovarian///characteristics_ch2.10: ///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Benign_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238212/GSM1238212_US22502615_251209754111_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-069///geo_accession: GSM1238213///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-069///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.1///characteristics_ch2.3: age at surgery: 57.43///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 101///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238213/GSM1238213_US22502615_251209749502_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-070///geo_accession: GSM1238214///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-070///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.9///characteristics_ch2.3: age at surgery: 80.93///characteristics_ch2.4: histology: Clear Cell///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 96///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238214/GSM1238214_US22502615_251209751009_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-071///geo_accession: GSM1238215///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-071///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 28.39///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 43///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238215/GSM1238215_US22502615_251209747450_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-072///geo_accession: GSM1238216///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-072///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.7///characteristics_ch2.3: age at surgery: 73.52///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIB///characteristics_ch2.6: grade: 1///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 36///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238216/GSM1238216_US22502615_251209754724_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-073///geo_accession: GSM1238217///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-073///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 65.23///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1023///characteristics_ch2.9: follow up months: 67///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Alive///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238217/GSM1238217_US22502615_251209754782_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-074///geo_accession: GSM1238218///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-074///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9///characteristics_ch2.3: age at surgery: 45.61///characteristics_ch2.4: histology: Benign///characteristics_ch2.5: tissue status: Benign///characteristics_ch2.6: disease status: Benign///characteristics_ch2.7: patient status: Benign///characteristics_ch2.8: disease state: Benign ovarian///characteristics_ch2.9: ///characteristics_ch2.10: ///characteristics_ch2.11: ///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Benign_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238218/GSM1238218_US22502615_251209747078_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-075///geo_accession: GSM1238219///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-075///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 72.21///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IC///characteristics_ch2.6: grade: 0///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 98///characteristics_ch2.9: disease status: Unknown///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238219/GSM1238219_US22502615_251209754148_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-076///geo_accession: GSM1238220///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-076///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8///characteristics_ch2.3: age at surgery: 67.35///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 37///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238220/GSM1238220_US22502615_251209754237_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-077///geo_accession: GSM1238221///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-077///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 48.15///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1027///characteristics_ch2.9: follow up months: 32///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Dead///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238221/GSM1238221_US22502615_251209754776_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-078///geo_accession: GSM1238222///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-078///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9///characteristics_ch2.3: age at surgery: 68.88///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 12///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238222/GSM1238222_US22502615_251209747449_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-079///geo_accession: GSM1238223///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-079///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.2///characteristics_ch2.3: age at surgery: 63.50///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 27///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238223/GSM1238223_US22502615_251209754155_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-080///geo_accession: GSM1238224///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-080///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 8.3///characteristics_ch2.3: age at surgery: 67.53///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 25///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238224/GSM1238224_US22502615_251209747092_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-081///geo_accession: GSM1238225///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-081///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.8///characteristics_ch2.3: age at surgery: 55.90///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 32///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238225/GSM1238225_US22502615_251209749836_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-082///geo_accession: GSM1238226///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-082///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 52.05///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Recurrence///characteristics_ch2.8: follow up months: 36///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238226/GSM1238226_US22502615_251209750955_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-083///geo_accession: GSM1238227///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-083///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.5///characteristics_ch2.3: age at surgery: 85.52///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IV///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 14///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238227/GSM1238227_US22502615_251209754808_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-084///geo_accession: GSM1238228///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-084///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 51.36///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 210///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238228/GSM1238228_US22502615_251209749355_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-085///geo_accession: GSM1238229///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-085///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 56.74///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 50///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238229/GSM1238229_US22502615_251209754088_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-086///geo_accession: GSM1238230///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-086///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.6///characteristics_ch2.3: age at surgery: 75.01///characteristics_ch2.4: histology: Endometrioid///characteristics_ch2.5: Stage: IIC///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 67///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238230/GSM1238230_US22502615_251209754135_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-087///geo_accession: GSM1238231///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-087///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.3///characteristics_ch2.3: age at surgery: 62.84///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC/IB///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 51///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238231/GSM1238231_US22502615_251209754787_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-088///geo_accession: GSM1238232///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-088///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 45.02///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIB///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1026///characteristics_ch2.9: follow up months: 50///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Alive///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238232/GSM1238232_US22502615_251209754151_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-089///geo_accession: GSM1238233///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-089///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.9///characteristics_ch2.3: age at surgery: 42.79///characteristics_ch2.4: histology: Mucinous///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 0///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 79///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Borderline ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Borderline_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238233/GSM1238233_US22502615_251209749024_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-090///geo_accession: GSM1238234///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-090///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 64.32///characteristics_ch2.4: histology: Endometrioid///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 211///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238234/GSM1238234_US22502615_251209754235_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-091///geo_accession: GSM1238235///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-091///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 10///characteristics_ch2.3: age at surgery: 64.85///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1119///characteristics_ch2.9: follow up months: 140///characteristics_ch2.10: disease status: Free///characteristics_ch2.11: patient status: Alive///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238235/GSM1238235_US22502615_251209750935_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-092///geo_accession: GSM1238236///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-092///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.6///characteristics_ch2.3: age at surgery: 44.53///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIA///characteristics_ch2.6: grade: 1///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 34///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238236/GSM1238236_US22502615_251209754798_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-093///geo_accession: GSM1238237///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-093///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 9.3///characteristics_ch2.3: age at surgery: 53.49///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: tcga id: TCGA-23-1102///characteristics_ch2.9: follow up months: 39///characteristics_ch2.10: disease status: Not Free///characteristics_ch2.11: patient status: Dead///characteristics_ch2.12: disease state: Malignant ovarian///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238237/GSM1238237_US22502615_251209747093_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-094///geo_accession: GSM1238238///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-094///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.4///characteristics_ch2.3: age at surgery: 63.21///characteristics_ch2.4: histology: Transitional Cell///characteristics_ch2.5: Stage: IIA///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 77///characteristics_ch2.9: disease status: Free///characteristics_ch2.10: patient status: Alive///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238238/GSM1238238_US22502615_251209754213_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-095///geo_accession: GSM1238239///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-095///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.9///characteristics_ch2.3: age at surgery: 68.12///characteristics_ch2.4: histology: Mucinous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 24///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238239/GSM1238239_US22502615_251209754154_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-096///geo_accession: GSM1238240///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-096///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: YES///characteristics_ch2.2: sample rin: 10///characteristics_ch2.3: age at surgery: 66.32///characteristics_ch2.4: histology: Endometrioid///characteristics_ch2.5: Stage: IA///characteristics_ch2.6: grade: 1///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 57///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238240/GSM1238240_US22502615_251209747077_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-097///geo_accession: GSM1238241///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-097///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 9.4///characteristics_ch2.3: age at surgery: 64.44///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 19///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238241/GSM1238241_US22502615_251209754166_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-098///geo_accession: GSM1238242///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-098///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.1///characteristics_ch2.3: age at surgery: 73.61///characteristics_ch2.4: histology: MMMT///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 3///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 17///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238242/GSM1238242_US22502615_251209754147_S01_A01.txt.gz///data_row_count: 20173
1
title: Ov_Tumor_Ref_Mix vs. CS-OV-099///geo_accession: GSM1238243///status: Public on Dec 26 2013///submission_date: Sep 23 2013///last_update_date: Dec 26 2013///type: RNA///channel_count: 2///source_name_ch1: 106 pooled ovarian samples///organism_ch1: Homo sapiens///characteristics_ch1: tissue: ovarian///characteristics_ch1.1: sample type: reference pool///molecule_ch1: total RNA///extract_protocol_ch1: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch1: Cy3///label_protocol_ch1: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch1: 9606///source_name_ch2: CS-OV-099///organism_ch2: Homo sapiens///characteristics_ch2: tissue: ovarian///characteristics_ch2.1: sample included in reference pool: NO///characteristics_ch2.2: sample rin: 8.7///characteristics_ch2.3: age at surgery: 68.22///characteristics_ch2.4: histology: Serous///characteristics_ch2.5: Stage: IIIC///characteristics_ch2.6: grade: 2///characteristics_ch2.7: tissue status: Primary///characteristics_ch2.8: follow up months: 14///characteristics_ch2.9: disease status: Not Free///characteristics_ch2.10: patient status: Dead///characteristics_ch2.11: disease state: Malignant ovarian///characteristics_ch2.12: ///molecule_ch2: total RNA///extract_protocol_ch2: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)///label_ch2: Cy5///label_protocol_ch2: Total RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)///taxid_ch2: 9606///hyb_protocol: Slides were incubated for 16-17 hr at 60C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.///scan_protocol: Scanned on an Agilent G2565BA scanner.///description: Malignant_ovarian_sample///data_processing: Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.///data_processing.1: Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1 (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.///platform_id: GPL7264///contact_name: Judy,,Dering///contact_email: jdering@mednet.ucla.edu///contact_laboratory: Translational Oncology Research///contact_department: Medicine///contact_institute: UCLA School of Medicine///contact_address: 2825 Santa Monica Blvd. Suite 200///contact_city: Santa Monica///contact_state: CA///contact_zip.postal_code: 90404///contact_country: USA///supplementary_file: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1238nnn/GSM1238243/GSM1238243_US22502615_251209749771_S01_A01.txt.gz///data_row_count: 20173
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(Other)
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Value
An expression set
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