metadata: metadata_22Q2

In UCLouvain-CBIO/depmap: Cancer Dependency Map Data Package

metadata_22Q2

Description

The 'metadata' dataset contains the metadata about cell lines in the 22Q2 Broad Institute DepMap release, which includes mapping between 'depmap_id' and 'cell_line' name for cancer cell lines. This dataset does not contain any data from the Achilles screen nor dependency data, but contains the metadata from the other datasets pertaining to the 22Q1 DepMap release, for 1840 cell lines, 0 genes, 33 primary diseases and 30 lineages. The columns of 'metadata' are: 'depmap_id', 'stripped_cell_line_name', 'cell_line', 'aliases', 'cosmic_id', 'sanger_id', 'WTSI_master_cell_ID', 'primary_disease', 'subtype_disease', 'sub_subtype_disease', 'gender', 'source' . This dataset can be loaded into the R environment with the 'depmap_metadata' function.

Usage

metadata

Format

A data frame with 1829 rows (cell lines) and 22 variables:

depmap_id

Cancer cell line primary key (i.e. "ACH-00001")

stripped_cell_line_name

Name of stripped cell line

cell_line

CCLE name of cancer cell line (i.e. "184A1_BREAST")

cell_line_name

Abbreviated name of cancer cell line (i.e. "NIH:OVCAR-3")

aliases

Aliases of cancer cell line

cosmic_id

Catalogue Of Somatic Mutations In Cancer ID number (e.g. 905933)

sex

Sex of tissue sample)

source

Source of tissue sample)

culture_type

Culture type of tissue sample)

RRID

Resource Identification Portal ID

sample_collection_site

Site of sample collection (AML), M3 (Promyelocytic))

primary_or_metastasis

Primary cancer cell line or metastatic

primary_disease

Primary Disease (e.g. cancer type)

subtype_disease

Subtype Disease (e.g. Acute Myelogenous Leukemia)

age

Age of individual sample of cell line was derived

sanger_id

Sanger ID (eg. 2201)

WTSI_master_cell_ID

Wellcome Trust Sanger Institute ID (eg. 1369)

additional_info

Additional information about samples

lineage

Lineage of cancer cell line

lineage_subtype

Subtype of lineage of cancer cell line

lineage_sub_subtype

Subtype of subtype of Lineage of cancer cell line

lineage_molecular_subtype

Molecular type of Lineage of cancer cell line

model_manipulation

Culture model manipulation details

model_manipulation_details

Culture model manipulation details

patient_id

Patient id

parent_patient_id

Parent patient id

Cellosaurus_NCIt_disease

Cellosaurus NCIt disease

Cellosaurus_NCIt_id

Cellosaurus NCIt_id

Cellosaurus_NCIt_id

Cellosaurus NCIt_id

Details

This data represents the 'sample_info.csv' file taken from the 22Q2 [Broad Institute](https://depmap.org/portal/download/) cancer depenedency study. This dataset features the a primary key 'depmap_id' which is a unique ID given to each cell line and is found in the first column of this dataset. The 'depmap_id' attribute is used as a foreign key in all other datasets in the package. This dataset has been converted to a long format tibble. This dataset does not contain any expression or dependency data but rather contains the metadata for all cancer cell lines used in the depmap project. Variables names were converted to lower case, put in snake case, and abbreviated where feasible (e.g. "Sanger ID" was changed to "sanger_id").

Change log

- 19Q1: Initial dataset consisted of data frame with 1677 rows (cell lines) and 9 variables, representing 0 genes, 1677 cell lines, 38 primary diseases and 33 lineages

- 19Q2: adds 37 new cell lines, 1 primary disease and 1 lineage. This version of the metadata dataset contains 6 variables not found in previous versions, relating the the Achilles metadata: 'Achilles_n_replicates', 'cell_line_NNMD', 'culture_type', 'culture_medium', and 'cas9_activity'.

- 19Q3: adds 30 cell lines, 2 primary diseases and 2 lineages

- 19Q4: adds 42 cell lines, 0 primary diseases and 3 lineages

- 20Q1: adds 19 cell lines, 'gender' was changed to 'sex', 'age', 'primary_or_metastasis' and 'sample_collection_site“ were added

- 20Q2: adds 30 cell lines and 1 lineage

- 20Q3: adds new column 'WTSI_master_cell_ID'

- 20Q4: adds 6 cell lines and 1 lineage. Adds column 'cell_line_name'

- 21Q1: removes 1 cell line

- 21Q2: adds 3 cell lines

- 21Q3: adds 1130 cell lines, 8 primary diseases and 8 lineages

- 21Q4: removes 1119 cell lines, 8 primary diseases and 8 lineages

- 22Q1: adds 4 cell lines. The features relating to Achilles metadata have been removed and put into their own dataset: 'Achilles_n_replicates', 'cell_line_NNMD', 'culture_type', 'culture_medium', and 'cas9_activity'.

- 22Q2: adds 11 cell lines and removes 2 primary diseases and 30 lineages. The feature 'culture_type' has been removed and columns "model_manipulation", "model_manipulation_details", "patient_id", "parent_depmap_id", "Cellosaurus_NCIt_disease", "Cellosaurus_NCIt_id" and "Cellosaurus_issues" have been added.

Source

DepMap, Broad Institute: https://depmap.org/portal/download/

References

Tsherniak, A., Vazquez, F., Montgomery, P. G., Weir, B. A., Kryukov, G., Cowley, G. S., ... & Meyers, R. M. (2017). Defining a cancer dependency map. Cell, 170(3), 564-576.

DepMap, Broad (2019): DepMap Achilles 19Q1 Public. https://figshare.com/articles/DepMap_Achilles_19Q1_Public/7655150

Robin M. Meyers, Jordan G. Bryan, James M. McFarland, Barbara A. Weir, ... David E. Root, William C. Hahn, Aviad Tsherniak. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nature Genetics 2017 October 49:1779–1784.

Mahmoud Ghandi, Franklin W. Huang, Judit Jané-Valbuena, Gregory V. Kryukov, ... Todd R. Golub, Levi A. Garraway & William R. Sellers. 2019. Next- generation characterization of the Cancer Cell Line Encyclopedia. Nature 569, 503–508 (2019).

Examples

## Not run: 
depmap_metadata()

## End(Not run)

UCLouvain-CBIO/depmap documentation built on Aug. 18, 2024, 9:46 p.m.