Supplementary Information for

It's DE-licious: a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR

Aaron T.L. Lun1,2, Yunshun Chen1,2 and Gordon K. Smyth1,3

1. Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research.
2. Department of Medical Biology,
3. Department of Mathematics and Statistics, The University of Melbourne.

Methods in Molecular Biology 1418, 391-416 (2016).
Preprint 8 April 2015

Summarized counts for the RNA-seq data

This page provides the summarized count data used for the case study in the book chapter by Lun et al (Preprint 8 April 2015). The data used in the book chapter are from a study on mouse mammary gland by Fu et al (PubMed). The raw sequence reads are available either in SRA format from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) as series GSE60450.

The study can be viewed as a 6-group experiment with 2 replicates for each combination of cell type and mouse status. The target information is provided below:

An Illumina HiSeq 2000 was used to create a FastQ file of 100bp paired-end sequence reads for each sample. The library size for each sample varied between 20 and 25 million. To obtain gene-level counts, fragments were mapped to the mm10 mouse genome using the Subread aligner, and fragment counts were summarized by Entrez Gene ID using the featureCounts function of the Bioconductor package Rsubread:

 

Comments/Questions? Contact Gordon Smyth.
Last modified: 19 January 2016