title: The complex transcriptional landscape of the anucleate human platelet.
abstract: BACKGROUND
  Human blood platelets are essential to maintaining normal hemostasis, and platelet dysfunction often causes bleeding or thrombosis. Estimates of genome-wide platelet RNA expression using microarrays have provided insights to the platelet transcriptome but were limited by the number of known transcripts. The goal of this effort was to deep-sequence RNA from leukocyte-depleted platelets to capture the complex profile of all expressed transcripts.
  
  
  RESULTS
  From each of four healthy individuals we generated long RNA (≥40 nucleotides) profiles from total and ribosomal-RNA depleted RNA preparations, as well as short RNA (<40 nucleotides) profiles. Analysis of ~1 billion reads revealed that coding and non-coding platelet transcripts span a very wide dynamic range (≥16 PCR cycles beyond β-actin), a result we validated through qRT-PCR on many dozens of platelet messenger RNAs. Surprisingly, ribosomal-RNA depletion significantly and adversely affected estimates of the relative abundance of transcripts. Of the known protein-coding loci, ~9,500 are present in human platelets. We observed a strong correlation between mRNAs identified by RNA-seq and microarray for well-expressed mRNAs, but RNASeq identified many more transcripts of lower abundance and permitted discovery of novel transcripts.
  
  
  CONCLUSIONS
  Our analyses revealed diverse classes of non-coding RNAs, including: pervasive antisense transcripts to protein-coding loci; numerous, previously unreported and abundant microRNAs; retrotransposons; and thousands of novel un-annotated long and short intronic transcripts, an intriguing finding considering the anucleate nature of platelets. The data are available through a local mirror of the UCSC genome browser and can be accessed at: http://cm.jefferson.edu/platelets_2012/.
authors: Cardeza Foundation for Hematologic Research, Division of Hematology, Department of Medicine, Thomas Jefferson University, Philadelphia, PA, USA. Paul.Bray@jefferson.edu
authors: Paul F
authors: PF
authors: Bray
authors: Steven E
authors: SE
authors: McKenzie
authors: Leonard C
authors: LC
authors: Edelstein
authors: Srikanth
authors: S
authors: Nagalla
authors: Kathleen
authors: K
authors: Delgrosso
authors: Adam
authors: A
authors: Ertel
authors: Joan
authors: J
authors: Kupper
authors: Yi
authors: Y
authors: Jing
authors: Eric
authors: E
authors: Londin
authors: Phillipe
authors: P
authors: Loher
authors: Huang-Wen
authors: HW
authors: Chen
authors: Paolo
authors: P
authors: Fortina
authors: Isidore
authors: I
authors: Rigoutsos
mesh_terms: D001792:Blood Platelets / Q000166:cytology* / Q000378:metabolism*; D002467:Cell Nucleus; D057225:Data Mining; D023281:Genomics; D006801:Humans; D020407:Internet; D007438:Introns / Q000235:genetics; D011544:Pseudogenes / Q000235:genetics; D016372:RNA, Antisense / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D016372:RNA, Antisense; D012333:RNA, Messenger; D012335:RNA, Ribosomal