title: Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats.
abstract: 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.
authors.affiliation: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University , Shanghai 201203, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University , Shanghai 201203, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Zhao
authors.affiliation: National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA.
authors.forename: Zhenqiang
authors.initials: Z
authors.lastname: Su
authors.affiliation: Center for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University , Loma Linda, California, 92350, USA.
authors.forename: Charles
authors.initials: C
authors.lastname: Wang
authors.affiliation: National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA.
authors.forename: James C
authors.initials: JC
authors.lastname: Fuscoe
authors.affiliation: National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA.
authors.forename: Weida
authors.initials: W
authors.lastname: Tong
authors.affiliation: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University , Shanghai 201203, China ; National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA ; Fudan-Zhangjiang Center for Clinical Genomics and Zhanjiang Center for Translational Medicine , Shanghai, 201203, China.
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
mesh_terms: D000367:Age Factors; D000818:Animals; D005260:Female; D020869:Gene Expression Profiling; D008297:Male; D009928:Organ Specificity; D012313:RNA / Q000235:genetics*; D011916:Rats, Inbred F344; D017423:Sequence Analysis, RNA; D012737:Sex Factors; D059467:Transcriptome
chemical_list: D012313:RNA