Files and links (1)
Published, Version of Record (VoR)CC BY V4.0, Open
Journal article
The complex transcriptional landscape of the anucleate human platelet
BMC genomics, v 14(1), pp 1-1
16 Jan 2013
PMID: 23323973
Featured in Collection : UN Sustainable Development Goals @ Drexel
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 similar to 1 billion reads revealed that coding and non-coding platelet transcripts span a very wide dynamic range (>= 16 PCR cycles beyond beta-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, similar to 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/.
Metrics
Details
- Title
- The complex transcriptional landscape of the anucleate human platelet
- Creators
- Paul F. Bray - Thomas Jefferson UniversitySteven E. McKenzie - Thomas Jefferson UniversityLeonard C. Edelstein - Thomas Jefferson UniversitySrikanth Nagalla - Thomas Jefferson UniversityKathleen Delgrosso - Kimmel Cancer CenterAdam Ertel - Sidney Kimmel Cancer CenterJoan Kupper - Kimmel Cancer CenterYi Jing - Thomas Jefferson UniversityEric Londin - Thomas Jefferson UniversityPhillipe Loher - Thomas Jefferson UniversityHuang-Wen Chen - Thomas Jefferson UniversityPaolo Fortina - Kimmel Cancer CenterIsidore Rigoutsos - Thomas Jefferson University
- Publication Details
- BMC genomics, v 14(1), pp 1-1
- Publisher
- Springer Nature
- Number of pages
- 15
- Grant note
- R01-HL-102482 / NIH-NHLBI; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Heart Lung & Blood Institute (NHLBI) TJU funds 2U19AI056363-06/2030984 / NIH-NIAID; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) R01HL102482 / NATIONAL HEART, LUNG, AND BLOOD INSTITUTE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Heart Lung & Blood Institute (NHLBI) P30-CA-56036 / NIH-NCI Cancer Center; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Cancer Institute (NCI) P30CA056036 / NATIONAL CANCER INSTITUTE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Cancer Institute (NCI) U19AI056363 / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) Kimmel Cancer Center (Philadelphia, PA) Cardeza Foundation for Hematological Research (Philadelphia, PA) William M. Keck Foundation; W.M. Keck Foundation
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000322386200001
- Scopus ID
- 2-s2.0-84872183938
- Other Identifier
- 991019176648504721
UN Sustainable Development Goals (SDGs)
This publication has contributed to the advancement of the following goals:
InCites Highlights
Data related to this publication, from InCites Benchmarking & Analytics tool:
- Web of Science research areas
- Biotechnology & Applied Microbiology
- Genetics & Heredity