title: Next generation sequencing analysis of human platelet PolyA+ mRNAs and rRNA-depleted total RNA.
abstract: BACKGROUND
  Platelets are small anucleate cells circulating in the blood vessels where they play a key role in hemostasis and thrombosis. Here, we compared platelet RNA-Seq results obtained from polyA+ mRNA and rRNA-depleted total RNA.
  
  
  METHODS
  We used purified, CD45 depleted, human blood platelets collected by apheresis from three male and one female healthy blood donors. The Illumina HiSeq 2000 platform was employed to sequence cDNA converted either from oligo(dT) isolated polyA+ RNA or from rRNA-depleted total RNA. The reads were aligned to the GRCh37 reference assembly with the TopHat/Cufflinks alignment package using Ensembl annotations. A de novo assembly of the platelet transcriptome using the Trinity software package and RSEM was also performed. The bioinformatic tools HTSeq and DESeq from Bioconductor were employed for further statistical analyses of read counts.
  
  
  RESULTS
  Consistent with previous findings our data suggests that mitochondrially expressed genes comprise a substantial fraction of the platelet transcriptome. We also identified high transcript levels for protein coding genes related to the cytoskeleton function, chemokine signaling, cell adhesion, aggregation, as well as receptor interaction between cells. Certain transcripts were particularly abundant in platelets compared with other cell and tissue types represented by RNA-Seq data from the Illumina Human Body Map 2.0 project. Irrespective of the different library preparation and sequencing protocols, there was good agreement between samples from the 4 individuals. Eighteen differentially expressed genes were identified in the two sexes at 10% false discovery rate using DESeq.
  
  
  CONCLUSIONS
  The present data suggests that platelets may have a unique transcriptome profile characterized by a relative over-expression of mitochondrially encoded genes and also of genomic transcripts related to the cytoskeleton function, chemokine signaling and surface components compared with other cell and tissue types. The in vivo functional significance of the non-mitochondrial transcripts remains to be shown.
authors.affiliation: Department of Clinical and Experimental Medicine, University of Linköping, Linköping, Sweden.
authors.forename: Antheia
authors.initials: A
authors.lastname: Kissopoulou
authors.affiliation: Department of Clinical and Experimental Medicine, University of Linköping, Linköping, Sweden.
authors.forename: Jon
authors.initials: J
authors.lastname: Jonasson
authors.affiliation: Department of Clinical and Experimental Medicine, University of Linköping, Linköping, Sweden.
authors.forename: Tomas L
authors.initials: TL
authors.lastname: Lindahl
authors.affiliation: Department of Clinical and Experimental Medicine, University of Linköping, Linköping, Sweden.
authors.forename: Abdimajid
authors.initials: A
authors.lastname: Osman
mesh_terms: D001483:Base Sequence; D001792:Blood Platelets / Q000737:chemistry* / Q000378:metabolism; D003599:Cytoskeleton / Q000737:chemistry / Q000378:metabolism; D005260:Female; D015870:Gene Expression; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017493:Leukocyte Common Antigens / Q000235:genetics / Q000378:metabolism; D008297:Male; D008928:Mitochondria / Q000737:chemistry* / Q000235:genetics; D008969:Molecular Sequence Data; D011061:Poly A / Q000737:chemistry* / Q000235:genetics; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D000077278:RNA, Mitochondrial; D012335:RNA, Ribosomal; D016415:Sequence Alignment; D015398:Signal Transduction; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger; D000077278:RNA, Mitochondrial; D012335:RNA, Ribosomal; D011061:Poly A; D012313:RNA; D017493:Leukocyte Common Antigens; C516769:PTPRC protein, human