Chickspress: A resource for chicken gene expression

Fiona M. McCarthy, Ken Pendarvis, Amanda M. Cooksey, Cathy R. Gresham, Matt Bomhoff, Sean Davey, Eric Lyons, Tad S. Sonstegard, Susan M. Bridges, Shane C. Burgess

Research output: Contribution to journalArticle

3 Scopus citations

Abstract

High-throughput sequencing and proteomics technologies are markedly increasing the amount of RNA and peptide data that are available to researchers, which are typically made publicly available via data repositories such as the NCBI Sequence Read Archive and proteome archives, respectively. These data sets contain valuable information about when and where gene products are expressed, but this information is not readily obtainable from archived data sets. Here we report Chickspress (http://geneatlas.arl.arizona.edu), the first publicly available gene expression resource for chicken tissues. Since there is no single source of chicken gene models, Chickspress incorporates both NCBI and Ensembl gene models and links these gene sets with experimental gene expression data and QTL information. By linking gene models from both NCBI and Ensembl gene prediction pipelines, researchers can, for the first time, easily compare gene models from each of these prediction workflows to available experimental data for these products. We use Chickspress data to show the differences between these gene annotation pipelines. Chickspress also provides rapid search, visualization and download capacity for chicken gene sets based upon tissue type, developmental stage and experiment type. This first Chickspress release contains 161 gene expression data sets, including expression of mRNAs, miRNAs, proteins and peptides. We provide several examples demonstrating how researchers may use this resource.

Original languageEnglish (US)
Article numberbaz058
JournalDatabase
Volume2019
Issue number1
DOIs
StatePublished - 2019

ASJC Scopus subject areas

  • Information Systems
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

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    McCarthy, F. M., Pendarvis, K., Cooksey, A. M., Gresham, C. R., Bomhoff, M., Davey, S., Lyons, E., Sonstegard, T. S., Bridges, S. M., & Burgess, S. C. (2019). Chickspress: A resource for chicken gene expression. Database, 2019(1), [baz058]. https://doi.org/10.1093/database/baz058