Dataset Information

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/.

SUBMITTER: Bray PF

PROVIDER: S-EPMC3722126 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature

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Publications

The complex transcriptional landscape of the anucleate human platelet.

Bray Paul F PF McKenzie Steven E SE Edelstein Leonard C LC Nagalla Srikanth S Delgrosso Kathleen K Ertel Adam A Kupper Joan J Jing Yi Y Londin Eric E Loher Phillipe P Chen Huang-Wen HW Fortina Paolo P Rigoutsos Isidore I

BMC genomics 20130116

<h4>Background</h4>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.<h4>Results</h4>From each of four ...[more]

PMID: 23323973

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Dataset Information

The complex transcriptional landscape of the anucleate human platelet.

Background

Results

Conclusions

Publications

The complex transcriptional landscape of the anucleate human platelet.

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