zhang.data: Bulk RNA-seq data from Zhang et al study.

In CenterForStatistics-UGent/PIMseq: PIM for testing differential expression in single cell RNA-seq data

Bulk RNA-seq data from Zhang et al study.

Description

498 neuroblastoma tumors, was retrieved from Zhang et al. (GEO accession number GSE49711). In short, unstranded poly(A)+ RNA sequencing was performed on the HiSeq 2000 instrument (Illumina). Paired-end reads with a length of 100 nucleotides were obtained. To quantify the full transcriptome, raw fastq files were processed with Kallisto v0.42.4 (index build with GRCh38-Ensembl v85). The pseudo-alignment tool Kallisto was chosen above other quantification methods as it is performing equally good but faster. For this study, a subset of 172 patients with high-risk disease were selected, forming two groups: the MYCN amplified (n1 = 91) and MYCN non-amplified (n2 = 81) tumors.

Usage

zhang.data

Format

A list object

Source

https://doi.org/10.1186/s13059-015-0694-1

References

Zhang W, Yu Y, Hertwig F, Thierry-Mieg J, Zhang W, Thierry-Mieg D, Wang J, Furlanello C, Devanarayan V, Cheng J, et al. Comparison of RNA-seq and microarray-based models for clinical endpoint prediction. Genome Biol. 2015;16(133) https://doi.org/10.1186/s13059-015-0694-1

counts

gene counts

group

MYCN (0 for MYCN non-amplified and 1 for MYCN amplified)

CenterForStatistics-UGent/PIMseq documentation built on Jan. 15, 2024, 3:49 a.m.