Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats

Sci Data. 2014 Jun 24;1:140013. doi: 10.1038/sdata.2014.13. eCollection 2014.


The rat is used extensively by the pharmaceutical, regulatory, and academic communities for safety assessment of drugs and chemicals and for studying human diseases; however, its transcriptome has not been well studied. As part of the SEQC (i.e., MAQC-III) consortium efforts, a comprehensive RNA-Seq data set was constructed using 320 RNA samples isolated from 10 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four ages (2-, 6-, 21-, and 104-week-old) with four biological replicates for each of the 80 sample groups (organ-sex-age). With the Ribo-Zero rRNA removal and Illumina RNA-Seq protocols, 41 million 50 bp single-end reads were generated per sample, yielding a total of 13.4 billion reads. This data set could be used to identify and validate new rat genes and transcripts, develop a more comprehensive rat transcriptome annotation system, identify novel gene regulatory networks related to tissue specific gene expression and development, and discover genes responsible for disease and drug toxicity and efficacy.

Publication types

  • Dataset
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Age Factors
  • Animals
  • Female
  • Gene Expression Profiling*
  • Male
  • Organ Specificity
  • RNA / genetics*
  • Rats, Inbred F344*
  • Sequence Analysis, RNA
  • Sex Factors
  • Transcriptome*


  • RNA