title: Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq.
abstract: RNA-Seq provides the capability to characterize the entire transcriptome in multiple levels including gene expression, allele specific expression, alternative splicing, fusion gene detection, and etc. The US FDA-led SEQC (i.e., MAQC-III) project conducted a comprehensive study focused on the transcriptome profiling of rat liver samples treated with 27 chemicals to evaluate the utility of RNA-Seq in safety assessment and toxicity mechanism elucidation. The chemicals represented multiple chemogenomic modes of action (MOA) and exhibited varying degrees of transcriptional response. The paired-end 100 bp sequencing data were generated using Illumina HiScanSQ and/or HiSeq 2000. In addition to the core study, six animals (i.e., three aflatoxin B1 treated rats and three vehicle control rats) were sequenced three times, with two separate library preparations on two sequencing machines. This large toxicogenomics dataset can serve as a resource to characterize various aspects of transcriptomic changes (e.g., alternative splicing) that are byproduct of chemical perturbation.
authors.affiliation: Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA.
authors.forename: Binsheng
authors.initials: B
authors.lastname: Gong
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: Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA.
authors.forename: Zhenqiang
authors.initials: Z
authors.lastname: Su
authors.affiliation: Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA.
authors.forename: Huixiao
authors.initials: H
authors.lastname: Hong
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, Maryland 20814, USA.
authors.forename: Jean
authors.initials: J
authors.lastname: Thierry-Mieg
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, Maryland 20814, USA.
authors.forename: Danielle
authors.initials: D
authors.lastname: Thierry-Mieg
authors.affiliation: Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA ; 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: Leming
authors.initials: L
authors.lastname: Shi
authors.affiliation: Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences , Research Triangle Park, North Carolina 27709, USA.
authors.forename: Scott S
authors.initials: SS
authors.lastname: Auerbach
authors.affiliation: Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA.
authors.forename: Weida
authors.initials: W
authors.lastname: Tong
authors.affiliation: Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA.
authors.forename: Joshua
authors.initials: J
authors.lastname: Xu
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D020869:Gene Expression Profiling; D015723:Gene Library; D008099:Liver; D012313:RNA / Q000235:genetics*; D051381:Rats; D059467:Transcriptome
chemical_list: D012313:RNA