Next generation sequencing analysis of human platelet PolyA+ mRNAs and rRNA-depleted total RNA

PloS One
Antheia KissopoulouAbdimajid Osman

Abstract

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. 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. 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 parti...Continue Reading

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Citations

Feb 3, 2016·Molecular Biology and Evolution·Cesare de FilippoAida M Andrés
Feb 19, 2017·Blood·Eric W MillsNicholas T Ingolia
Mar 30, 2017·Platelets·Abdimajid OsmanPatrick Provost
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Datasets Mentioned

BETA
ERS025084
E-MTAB-715
E-MTAB-1846

Methods Mentioned

BETA
RNA-Seq
RNASeq
GTPase
PCR
Assay

Software Mentioned

Trinity
HTSeq
Trinity RNA - Seq
Illumina
Serial Analysis of Gene Expression ( SAGE )
R
Bowtie
SAGE
bwa
RSEM

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