title: High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping.
abstract: BACKGROUND
  We present a genome-wide messenger RNA (mRNA) sequencing technique that converts small amounts of RNA from many samples into molecular phenotypes. It encompasses all steps from sample preparation to sequence analysis and is applicable to baseline profiling or perturbation measurements.
  
  
  RESULTS
  Multiplex sequencing of transcript 3' ends identifies differential transcript abundance independent of gene annotation. We show that increasing biological replicate number while maintaining the total amount of sequencing identifies more differentially abundant transcripts.
  
  
  CONCLUSIONS
  This method can be implemented on polyadenylated RNA from any organism with an annotated reference genome and in any laboratory with access to Illumina sequencing.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
authors.forename: John E
authors.initials: JE
authors.lastname: Collins
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
authors.forename: Neha
authors.initials: N
authors.lastname: Wali
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
authors.forename: Ian M
authors.initials: IM
authors.lastname: Sealy
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
authors.forename: James A
authors.initials: JA
authors.lastname: Morris
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: White
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
authors.forename: Steven R
authors.initials: SR
authors.lastname: Leonard
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
authors.forename: David K
authors.initials: DK
authors.lastname: Jackson
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Jones
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
authors.forename: Nathalie C
authors.initials: NC
authors.lastname: Smerdon
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
authors.forename: Jorge
authors.initials: J
authors.lastname: Zamora
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Dooley
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
authors.forename: Samantha N
authors.initials: SN
authors.lastname: Carruthers
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
authors.forename: Jeffrey C
authors.initials: JC
authors.lastname: Barrett
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. ds4@sanger.ac.uk.
authors.forename: Derek L
authors.initials: DL
authors.lastname: Stemple
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. emb@sanger.ac.uk.
authors.forename: Elisabeth M
authors.initials: EM
authors.lastname: Busch-Nentwich
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods; D015723:Gene Library; D056726:Genetic Association Studies / Q000379:methods; D055106:Genome-Wide Association Study / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D058889:Molecular Typing / Q000379:methods; D009154:Mutation; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA; D015027:Zebrafish
chemical_list: D012333:RNA, Messenger