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Series GSE38056 Query DataSets for GSE38056
Status Public on Jun 30, 2013
Title Novel long non-coding RNAs are involved in cellular response to angiotensin II signaling
Organism Rattus norvegicus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Angiotensin II (AngII) is a polypeptide hormone that plays a pivotal role in the regulation of blood pressure. In vascular smooth muscle cells (VSMCs), AngII signaling results in hypertrophy, proliferation, contraction, and migration, which ultimately promote atherosclerosis and hypertensive cardiovascular diseases. Recent studies have shown that fundamental biological processes such as cell proliferation and differentiation are mediated in part by the activities of long non-protein-coding RNAs (lncRNAs). In this study, we sought to identify lncRNAs that are involved in the response to AngII-signaling. Genome-wide analysis of de novo assembled transcripts from rat vascular smooth muscle cells (VSMCs) identified novel lncRNA as well as protein-coding transcripts which have not been previously annotated. The majority of the genomic loci from which these novel transcripts are transcribed are enriched for histone H3 lysine 4 trimethylation and histone H3 lysine 36 trimethylation, two chromatin modifications that are closely associated with actively transcribed regions, further supporting these as bona fide transcripts. Compared with previously annotated rat transcripts, these novel lncRNA transcripts, on average, are shorter in length and are less abundant, consistent with reports from mice and humans. Expression analyses of transcripts from control and AngII-stimulated VSMCs reveal that AngII signaling affects the abundance of both protein-coding transcripts as well as lncRNAs transcripts. Altogether, these data provide new insights into the global effects of AngII signaling and reveal potential novel therapeutic targets for treatment of AngII-associated cardiovascular diseases.
 
Overall design RNA-sequencing of control and AngII (3hrs)-stimulated rVSMSCs. ChIP-sequencing of H3K4me3 and H3K36me3 in control and AngII (3hrs)-stimulated rVSMCs.
 
Contributor(s) Leung A, Schones DE, Natarajan RN, Lanting L, Trac C
Citation(s) 23697773, 34685676
Submission date May 18, 2012
Last update date Oct 27, 2021
Contact name Amy Leung
Organization name Beckman Research Institute, City of Hope
Department Diabetes/Cancer
Lab Schones
Street address 1500 E. Duarte Rd
City Duarte
ZIP/Postal code 91010
Country USA
 
Platforms (2)
GPL10287 Illumina Genome Analyzer II (Rattus norvegicus)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
Samples (8)
GSM933094 Control_H3K4me3_ChIPseq
GSM933095 Control_H3K36me3_ChIPseq
GSM933096 Control_Input_ChIPseq
Relations
BioProject PRJNA167134
SRA SRP013262

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE38056_RAW.tar 4.1 Mb (http)(custom) TAR (of BED, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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