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

Scientific Data

Volumn 1, Issue , 2014, Pages

  Yu, Ying ^a   Zhao, Chen ^a   Su, Zhenqiang ^b   Wang, Charles ^c   Fuscoe, James C ^b   Tong, Weida ^b   Shi, Leming ^a,b,d  

^a FUDAN UNIVERSITY   (China)

^b NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

^c LOMA LINDA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d Center for Translational Medicine   (China)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; TRANSCRIPTOME;

AGE; ANIMAL; ANTIBODY SPECIFICITY; FEMALE; FISCHER 344 RAT; GENE EXPRESSION PROFILING; GENETICS; MALE; SEQUENCE ANALYSIS; SEX DIFFERENCE;

AGE FACTORS; ANIMALS; FEMALE; GENE EXPRESSION PROFILING; MALE; ORGAN SPECIFICITY; RATS, INBRED F344; RNA; SEQUENCE ANALYSIS, RNA; SEX FACTORS; TRANSCRIPTOME;

EID: 84960885434     PISSN: None     EISSN: 20524463     Source Type: Journal    
DOI: 10.1038/sdata.2014.13     Document Type: Article

References (17)

1. Roy, S. et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330, 1787-1797 (2010).
2. Mardis, E. R. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9, 387-402 (2008).
3. Metzker, M. L. Sequencing technologies-the next generation. Nat. Rev. Genet. 11, 31-46 (2010).
4. Morozova, O., Hirst, M., Marra, M. A. Applications of new sequencing technologies for transcriptome analysis. Annu. Rev. Genomics Hum. Genet. 10, 135-151 (2009).
5. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628 (2008).
6. Celniker, S. E. et al. Unlocking the secrets of the genome. Nature 459, 927-930 (2009).
7. Gerstein, M. B. et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330, 1775-1787 (2010).
8. Yu, Y. et al. A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages. Nat. Commun. 5, 3230 (2014).
9. Qing, T., Yu, Y., Du, T., Shi, L. mRNA enrichment protocols determine the quantification characteristics of external RNA spikein controls in RNA-Seq studies. Sci. China Life Sci. 56, 134-142 (2013).
10. Thierry-Mieg, D., Thierry-Mieg, J. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol. 7(S12): 11-14 (2006).
11. Kwekel, J. C., Desai, V. G., Moland, C. L., Branham, W. S., Fuscoe, J. C. Age and sex dependent changes in liver gene expression during the life cycle of the rat. BMC Genomics 11, 675 (2010).
12. Langmead, B., Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
13. Lohse, M. et al. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res. 40, W622-W627 (2012).
14. Trapnell, C., Pachter, L., Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
15. Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562-578 (2012).
16. R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing (2012).
17. Hansen, K. D., Brenner, S. E., Dudoit, S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res. 38, e131 (2010).