RNA-seq reveals novel transcriptome of genes and their isoforms in human pulmonary microvascular endothelial cells treated with thrombin.

PloS One
Li Qin ZhangShui Qing Ye

Abstract

The dysregulation of vascular endothelial cells by thrombin has been implicated in the development of a number of pathologic disorders such as inflammatory conditions, cancer, diabetes, coronary heart disease. However, transcriptional regulation of vascular endothelial cells by thrombin is not completely understood. In the present study, Illumina RNA-seq was used to profile the transcriptome in human pulmonary microvascular endothelial cells (HMVEC-L) treated with thrombin for 6 h to gain insight into thrombin's direct effects on the endothelial function. Out of 100 million total reads from a paired end sequencing assay, 91-94% of the reads were aligned to over 16,000 genes in the reference human genome. Thrombin upregulated 150 known genes and 480 known isoforms, and downregulated 2,190 known genes and 3,574 known isoforms by at least 2 fold. Of note, thrombin upregulated 1,775 previously unknown isoforms and downregulated 12,202 previously unknown isoforms by at least 2 fold. Many genes displayed isoform specific differential expression levels and different usage of transcriptional start sites after the thrombin treatment. The cross comparisons between our RNA-seq data and those of DNA microarray analysis of either 6 h thromb...Continue Reading

References

Apr 10, 1997·The New England Journal of Medicine·P J Barnes, M Karin
Jul 25, 2000·Developmental Dynamics : an Official Publication of the American Association of Anatomists·M J Beanan, T D Sargent
Sep 8, 2000·The Journal of Biological Chemistry·L BarberisF G Giancotti
Dec 5, 2000·Matrix Biology : Journal of the International Society for Matrix Biology·P L Jones, F S Jones
Mar 21, 2002·The Lancet Oncology·G F NashA K Kakkar
Apr 17, 2003·Current Topics in Developmental Biology·Wadie F Bahou
Oct 11, 2003·Arteriosclerosis, Thrombosis, and Vascular Biology·Takashi MinamiWilliam C Aird
May 7, 2004·The Journal of Immunology : Official Journal of the American Association of Immunologists·Alexander D BarrowJohn Trowsdale
Apr 12, 2006·Proceedings of the National Academy of Sciences of the United States of America·Barbara UzonyiAndreas J R Habenicht
Apr 18, 2006·Journal of Leukocyte Biology·Dorothee ViemannJohannes Roth
Oct 16, 2007·Current Opinion in Cell Biology·Hirofumi Morishita, Takeshi Yagi
Feb 19, 2008·Thrombosis and Haemostasis·Lluis MartorellLina Badimon
Mar 28, 2008·American Journal of Physiology. Cell Physiology·Panagiota ZaniaNikos E Tsopanoglou
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Jul 23, 2008·Perspectives in Vascular Surgery and Endovascular Therapy·Kimon Bekelis, Nicos Labropoulos
Dec 19, 2008·Angiogenesis·Guoquan LiuTatyana A Voyno-Yasenetskaya
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Jun 9, 2009·Cytokine & Growth Factor Reviews·Laurent DavidSabine Bailly
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jul 1, 2009·Expert Reviews in Molecular Medicine·Puneet KumarSarah Y Yuan
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Feb 20, 2010·European Cytokine Network·Nikos E Tsopanoglou, Michael E Maragoudakis
Mar 29, 2011·Blood·Montaser ShaheenRobert Hromas
May 3, 2011·Immunobiology·Ghada S HassanWalid Mourad
Jun 18, 2011·Nature Reviews. Genetics·John W DaveyMark L Blaxter
Jul 21, 2011·Nature Immunology·Yinon Ben-Neriah, Michael Karin
Aug 23, 2011·Molecular and Cellular Biochemistry·Milan PopovićEsma R Isenović

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Citations

Mar 22, 2014·BMC Medical Genomics·Qu ZhangSitong Sheng
Mar 19, 2013·BMC Medical Genetics·Hongzhuan YinQi Su
Oct 25, 2012·Bioinformatics·Matteo BenelliAlberto Magi
Dec 25, 2012·Cell & Bioscience·Daniel P HeruthShui Qing Ye
Sep 18, 2012·Progress in Retinal and Eye Research·Arpita S BharadwajJustine R Smith
Feb 12, 2017·American Journal of Respiratory Cell and Molecular Biology·Yimu YangEric P Schmidt
Feb 18, 2018·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Guangliang BiShui Qing Ye
Sep 3, 2013·The Journal of Immunology : Official Journal of the American Association of Immunologists·Amin Al-ShamiTamas Oravecz
Feb 9, 2017·Source Code for Biology and Medicine·Yan Li, Jorge Andrade
May 3, 2014·Molecular Medicine Reports·Xiuhui WangBeigang Fu

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Datasets Mentioned

BETA
SRA046349.2

Methods Mentioned

BETA
RNA-Seq
RNASeq
chips
Chip
RNA Seq

Software Mentioned

Sigmaplot
Cufflinks
Systat
Data Assist
Illumina Off - Line Basecaller ( OLB )
Cuffdiff
Ingenuity Pathway Analysis
Integrative Genomics Viewer
Epoch
igvtools

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