zhang.data.sub: Neuroblastoma bulk RNA-seq data retrieved from Zhang et...

In CenterForStatistics-UGent/SPsimSeq: Semi-parametric simulation tool for bulk and single-cell RNA sequencing data

Neuroblastoma bulk RNA-seq data retrieved from Zhang et (2015).

Description

The data contains 498 neuroblastoma tumors. 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 tumors (samples) with high-risk disease were selected, forming two groups: the MYCN amplified ($n_1$ = 91) and MYCN non-amplified ($n_2$ = 81) tumours. Sometimes we refer this dataset to us the Zhang data or the Zhang neuroblastoma data. In this package, a subset of 5000 genes (randomly selected) are made available for illustration purpose only.

Usage

data(zhang.data.sub)

Format

A list object

Source

GEO accession GSE49711

References

1. 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 2. Assefa, A. T., De Paepe, K., Everaert, C., Mestdagh, P., Thas, O., & Vandesompele, J. (2018). Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data. GENOME BIOLOGY, 19.

counts

gene counts

group

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

Examples

data("zhang.data.sub")
str(zhang.data.sub)

CenterForStatistics-UGent/SPsimSeq documentation built on Nov. 21, 2024, 6:30 a.m.