Supporting data for "Digital Expression Explorer 2: a repository of uniformly processed RNA sequencing data"

RNA-seq is an indispensable tool in the study of gene regulation. While the technology has brought with it better transcript coverage and quantification, there remain considerable barriers-to-entry for the computational biologist to analyze large data sets. There is a real need for a repository of uniformly processed RNA-seq data that is easy to use. <br>To address these obstacles, we developed Digital Expression Explorer 2 (DEE2), a web-based repository of RNA-seq data in the form of gene-level and transcript-level expression counts. DEE2 contains over 5.3 trillion assigned reads from 580,000 RNA-seq data sets including species E. coli, yeast, Arabidopsis, worm, fruit fly, zebrafish, rat, mouse and human. Base-space sequence data downloaded from NCBI Sequence Read Archive underwent quality control prior to transcriptome and genome mapping using open-source tools. Uniform data processing methods ensure consistency across experiments, facilitating fast and reproducible meta-analyses. <br>The web interface allows users to quickly identify data sets of interest using accession number and keyword searches. The data can also be accessed programmatically using a specifically designed R package. We demonstrate that DEE2 data is compatible with statistical packages such as edgeR or DESeq. Bulk data are also available for download. DEE2 can be found at DEE2.io