Poster Open Access

Digital Expression Explorer 2: a repository of 4.5 trillion uniformly processed RNA-seq reads and counting

Ziemann, Mark; Kaspi, Antony; El-Osta, Assam


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  <dc:creator>Ziemann, Mark</dc:creator>
  <dc:creator>Kaspi, Antony</dc:creator>
  <dc:creator>El-Osta, Assam</dc:creator>
  <dc:date>2018-11-27</dc:date>
  <dc:description>Background: Transcriptome profiling by RNA-seq has enhanced scientific understanding of gene regulation. Despite the benefits these data have brought in terms of transcriptome coverage and accuracy, there are considerable barriers-to-entry for the novice computational biologist to analyse these large data sets. There is a definite need for a repository of uniformly processed RNA-seq data that is easy to use and represents major model organisms. Findings: 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 400,000 RNA-seq data sets from several species including yeast, Arabidopsis, worm, fruit fly, zebrafish, rat, mouse and human. Base-space sequence data downloaded from NCBI Sequence Read Archive underwent quality analysis, filtering and trimming prior to transcriptome and genome alignment and read counting using open-source tools. Uniform reference-genome and data processing methods ensure consistency across experiments, facilitating fast and reproducible meta-analyses. Conclusions: The web interface enables users to quickly identify data sets of interest through accession number and keyword searches. These data can also be accessed programmatically using a specifically designed R script. We demonstrate how DEE2 data is compatible with statistical packages such as edgeR or DESeq. DEE2 can be found at http://dee2.io</dc:description>
  <dc:identifier>https://zenodo.org/record/1561840</dc:identifier>
  <dc:identifier>10.5281/zenodo.1561840</dc:identifier>
  <dc:identifier>oai:zenodo.org:1561840</dc:identifier>
  <dc:relation>doi:10.5281/zenodo.1561839</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>http://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  <dc:subject>ABACBS2018</dc:subject>
  <dc:title>Digital Expression Explorer 2: a repository of 4.5 trillion uniformly processed RNA-seq reads and counting</dc:title>
  <dc:type>info:eu-repo/semantics/conferencePoster</dc:type>
  <dc:type>poster</dc:type>
</oai_dc:dc>
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