title: ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets.
abstract: BACKGROUND
  RNA sequencing is a flexible and powerful new approach for measuring gene, exon, or isoform expression. To maximize the utility of RNA sequencing data, new statistical methods are needed for clustering, differential expression, and other analyses. A major barrier to the development of new statistical methods is the lack of RNA sequencing datasets that can be easily obtained and analyzed in common statistical software packages such as R. To speed up the development process, we have created a resource of analysis-ready RNA-sequencing datasets. 2 DESCRIPTION: ReCount is an online resource of RNA-seq gene count tables and auxilliary data. Tables were built from raw RNA sequencing data from 18 different published studies comprising 475 samples and over 8 billion reads. Using the Myrna package, reads were aligned, overlapped with gene models and tabulated into gene-by-sample count tables that are ready for statistical analysis. Count tables and phenotype data were combined into Bioconductor ExpressionSet objects for ease of analysis. ReCount also contains the Myrna manifest files and R source code used to process the samples, allowing statistical and computational scientists to consider alternative parameter values. 3 CONCLUSIONS: By combining datasets from many studies and providing data that has already been processed from. fastq format into ready-to-use. RData and. txt files, ReCount facilitates analysis and methods development for RNA-seq count data. We anticipate that ReCount will also be useful for investigators who wish to consider cross-study comparisons and alternative normalization strategies for RNA-seq.
authors.affiliation: Department of Biostatistics, The Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA.
authors.forename: Alyssa C
authors.initials: AC
authors.lastname: Frazee
authors.forename: Ben
authors.initials: B
authors.lastname: Langmead
authors.forename: Jeffrey T
authors.initials: JT
authors.lastname: Leek
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D012313:RNA / Q000032:analysis* / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA
references.citation: Nature. 2010 Apr 1;464(7289):768-72
references.pmid: 20220758
references.citation: Am J Hum Genet. 2007 Mar;80(3):502-9
references.pmid: 17273971
references.citation: Genetics. 2010 Jun;185(2):405-16
references.pmid: 20439781
references.citation: Genome Res. 2010 Jun;20(6):847-60
references.pmid: 20452967
references.citation: Nature. 2008 Nov 27;456(7221):470-6
references.pmid: 18978772
references.citation: Genome Biol. 2010;11(5):207
references.pmid: 20441614
references.citation: PLoS Biol. 2010 Sep 14;8(9):
references.pmid: 20856902
references.citation: Genome Res. 2009 Apr;19(4):657-66
references.pmid: 19181841
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: Genome Biol. 2010;11(8):R83
references.pmid: 20701754
references.citation: Nature. 2011 Mar 24;471(7339):473-9
references.pmid: 21179090
references.citation: Genome Res. 2010 May;20(5):614-22
references.pmid: 20363980
references.citation: Bioinformatics. 2003 Jan 22;19(2):185-93
references.pmid: 12538238
references.citation: PLoS One. 2011 Mar 24;6(3):e17820
references.pmid: 21455293
references.citation: Science. 2008 Aug 15;321(5891):956-60
references.pmid: 18599741
references.citation: Nat Biotechnol. 2011 Jul 11;29(7):572-3
references.pmid: 21747377
references.citation: Nat Biotechnol. 2010 May;28(5):511-5
references.pmid: 20436464
references.citation: BMC Bioinformatics. 2010 Feb 18;11:94
references.pmid: 20167110
references.citation: Science. 2008 Dec 19;322(5909):1845-8
references.pmid: 19056941
references.citation: Nat Genet. 2007 Feb;39(2):226-31
references.pmid: 17206142
references.citation: Nat Methods. 2010 Dec;7(12):1009-15
references.pmid: 21057496
references.citation: Nature. 2010 Apr 1;464(7289):773-7
references.pmid: 20220756
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D19-21
references.pmid: 21062823
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D1005-10
references.pmid: 21097893
references.citation: Science. 2008 Jun 6;320(5881):1344-9
references.pmid: 18451266
references.citation: Nat Rev Genet. 2009 Jan;10(1):57-63
references.pmid: 19015660
references.citation: Genome Biol. 2004;5(10):R80
references.pmid: 15461798
references.citation: Genome Res. 2010 Feb;20(2):180-9
references.pmid: 20009012
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D800-6
references.pmid: 21045057