Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Long non-coding RNA profiling in 6 cell types

ABSTRACT: To identify endothelial cell (EC)-enriched long noncoding RNAs (lncRNAs), gene expression analysis was conducted on two EC cell types and 4 non-EC cell types. Specifically, the EC cell types were human umbilical vein endothelial cells (HUVEC) and human dermal microvascular endothelial cells (HMVEC). The 4 non-EC cell types were human aortic smooth muscle cells (HASMC), Fibroblasts, Hepatocytes, and keratinocytes. Of the 23 155 putative lncRNAs represented in the custom lncRNA microarrays, 18 524 lncRNAs were found to be expressed above the 20% percentile in at least one cell type. Importantly, 28 EC-enriched lncRNAs were identified in common between HUVEC and HMVEC with 28 and 59 enriched uniquely in either HUVEC or HMVEC, respectively. Of interest, STEEL, an EC-enriched lncRNA was identified and its role in EC biology was further characterized.

ORGANISM(S): Homo sapiens

PROVIDER: GSE108318 | GEO | 2018/03/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Expression profiling of Endothelial (EC) and Non-endothelial Cells

Project description:Gene expression profiling of HUVEC (human umbilical vein EC cell; Lonza), HAEC (human aortic EC cells), HCAEC (human coronary artery EC cells), HPAEC (human pulmonary artery EC cells), HMVEC (human microvascular (dermal) , HASMC ( Human Aortic Smooth Muscle Cells), T cells and Bcells. Gene expression profiling of Endothelial cells and Non-endothelial cells in order to identify the genes with preferntial expression to endothelial cells. The experiments are performed in duplicate on both the HT Human Genome U133A and U133B arrays.

2011-04-04 | E-GEOD-21212 | biostudies-arrayexpress

Angiogenic patterning by STEEL, an endothelial-enriched long noncoding RNAAngiogenic patterning by STEEL, an endothelial-enriched long noncoding RNA

Project description:Endothelial cell (EC)-enriched protein coding genes, such as endothelial nitric oxide synthase (eNOS), define quintessential EC-specific physiologic functions. It is not clear whether long noncoding RNAs (lncRNAs) also define cardiovascular cell-type specific phenotypes, especially in the vascular endothelium. Here, we report the existence of a set of EC-enriched lncRNAs and define a role for STEEL (spliced transcript – endothelial enriched lncRNA) in angiogenic potential, macrovascular/microvascular identity and shear stress responsiveness. STEEL is expressed from the terminus of the HOXD locus and is transcribed antisense to HOXD transcription factors. STEEL RNA increases the number and integrity of de novo perfused microvessels in an in vivo model and augments angiogenesis in vitro. The STEEL RNA is polyadenylated, nuclear-enriched and has microvascular predominance. Functionally, STEEL regulates a number of genes in diverse endothelial cells. Of interest, STEEL upregulates both eNOS and the transcription factor Kruppel-like factor 2 (KLF2), and is subject to feedback inhibition by both eNOS and shear-augmented KLF2. Mechanistically, STEEL upregulation of eNOS and KLF2 is transcriptionally mediated, in part, via interaction of chromatin-associated STEEL with the poly-ADP ribosylase, PARP1. For instance, STEEL recruits PARP1 to the KLF2 promoter. This work identifies a role for EC-enriched lncRNAs in the phenotypic adaptation of ECs to both body position and hemodynamic forces, and establishes a newer role for lncRNAs in the transcriptional regulation of EC identity.

2018-02-28 | PXD008581 | Pride

Comparison of STEEL siRNA-treated and control siRNA-treated human endothelial cells

Project description:To determine the role of STEEL in endothelial cell (EC) gene regulation, gene expression analysis was conducted on control and STEEL siRNA-treated human dermal microvascular endothelial cells (HMVECs) and human umbilical vein endothelial cells (HUVECs). A total of 225 protein-coding genes were downregulated and 80 were upregulated when both EC types were grouped for analysis. In HMVEC alone, 544 protein-coding genes were downregulated and 218 were upregulated. In HUVEC alone, 177 protein-coding genes were downregulated and 125 were upregulated. Prominently, STEEL siRNA depletion results in the downregulation of two notable protein-coding genes, eNOS and KLF2, which are modulated in ECs subjected to continuous laminar shear stress.

2018-03-30 | GSE108262 | GEO

Comparative study of mRNAs and lncRNAs in endothelial and non-endothelial cells

Project description:To identify lncRNAs enriched in ECs, a microarray was performed to profile ~30,000 lncRNAs and ~26,000 coding transcripts using an Arraystar human LncRNA microarray v3.0 system (Arraystar, Rockville, MD). Three primary human EC lines and two non-EC lines at low passages, namely, human umbilical vein EC (HUVEC), human retinal EC (HREC), human choroidal EC, human dermal fibroblast cell (HDF) and human retinal pigment epithelial (RPE) cell lines, were used in the array. Purity of EC lines was confirmed by acetyl-LDL uptake and EC marker staining

2018-10-08 | GSE105107 | GEO

Expression profiling of Endothelial (EC) and Non-endothelial Cells

2011-04-04 | GSE21212 | GEO

Transcription profiling of human endothelial and fibroblast cells isolated from umbilical cord veins treated with interferons to identify genes regulated by interferons

Project description:IFNs are highly pleiotropic cytokines also endowed with marked anti-angiogenic activity. In this study, the mRNA expression profiles of endothelial cells (EC) exposed in vitro to IFN-alpha, IFN-beta, or; IFN-gamma were determined. We found that in HUVEC as well as in other EC types 175 genes were upregulated (>2-fold increase) by IFNs, including genes involved in the host response to RNA viruses, inflammation, and apoptosis. Interestingly, 41 genes showed a >5-fold higher induction by IFN-alpha in EC compared to human fibroblasts; among them, the gene encoding the angiostatic chemokine CXCL11 was selectively induced by IFN-alpha in EC along with other genes associated; with angiogenesis regulation, including CXCL10, TRAIL, and guanylate binding protein 1 (GBP-1). These transcriptional changes were confirmed and extended by quantitative PCR analysis and ELISA; whereas IFN-alpha and IFN-beta exerted virtually identical effects on transcriptome modulation, a differential gene regulation by type I and type II IFN emerged, especially as far as quantitative aspects were concerned. In vivo, IFN-alpha-producing tumors over-expressed murine CXCL10-11,; GBP-1 and TRAIL, with evidence of CXCL11 production by tumor-associated EC. Overall, these findings improve our understanding of the anti-angiogenic effects of IFNs by showing that these cytokines trigger an anti-angiogenic transcriptional program in EC. Moreover, we suggest that quantitative differences in the magnitude of the transcriptional activation of IFNresponsive genes could form the basis for cell-specific transcriptional signatures. In press, J. Immunol. 2007. Experiment Overall Design: comparison of interferon effects on endothelial cells (HUVEC, HMVEC) and fibrobloasts

2009-04-08 | E-GEOD-3920 | biostudies-arrayexpress

Identifying target genes for the long noncoding RNA, GATA2-AS1

Project description:We have identified a set of endothelial-enriched long noncoding RNAs (lncRNAs) in another experiment. In this experiment, we aim to identify genes that are regulated by the GATA2-AS1 lncRNA. We have depleted GATA2-AS1 using two distinct siRNA in human umbilical vein endothelial cells (HUVEC)

2022-02-25 | GSE197376 | GEO

Transcriptome analysis of human embryonic stem cell differentiation to endothelial cells

Project description:Deep RNA sequencing was performed during human embryonic stem cell (hESC) differentiation to endothelial cells (ECs), via mesodermal precursors. Our work focused on long non-coding RNAs (lncRNAs) regulated during EC differentiation as lncRNA are known regulators of cell differentiation, physiology and disease. EC-enriched lncRNAs were screened for binding sites for the transcription factor ERG, important for endothelial cell identity and function. The LINC00961 gene, first annotated as a lncRNA but now reassigned as a protein coding gene for the SPAAR micropeptide, was potently activated during differentiation. Using primary ECs, we studied the role of LINC00961 locus after depletion and gain of function experiments and showed its effect on EC adhesion, tube formation, migration and proliferation. We showed that LINC00961 functions as a bona fide non-coding RNA in ECs, at least in part, through binding to TMSB4X.

2020-03-23 | GSE118106 | GEO

Implication of Long noncoding RNAs in the endothelial cell response to hypoxia II.

Project description:Long noncoding RNAs (lncRNAs) are non-protein coding RNAs regulating gene expression. Although for some lncRNAs a relevant role in hypoxic endothelium has been shown, the regulation and function of lncRNAs is still largely unknown in the vascular physio-pathology. Taking advantage of next-generation sequencing techniques, transcriptomic changes induced by endothelial cell exposure to hypoxia were investigated. Paired-end sequencing of polyadenylated RNA derived from human umbilical vein endothelial cells (HUVECs) exposed to 1% O2 or normoxia was performed. Bioinformatics analysis identified â 2000 differentially expressed genes, including 122 lncRNAs. Extensive validation was performed by both microarray and qPCR. Among the validated lncRNAs, H19, MIR210HG, MEG9, MALAT1 and MIR22HG were also induced in a mouse model of hindlimb ischemia. To test the functional relevance of lncRNAs in endothelial cells, knockdown of H19 expression was performed. H19 inhibition decreased HUVEC growth, inducing their accumulation in G1 phase of the cell cycle; accordingly, p21 (CDKN1A) expression was increased. Additionally, H19 knockdown also diminished HUVEC ability to form capillary like structures when plated on matrigel. In conclusion, a high-confidence signature of lncRNAs modulated by hypoxia in HUVEC was identified and a significant impact of H19 lncRNA was shown. HUVEC were exposed to normoxia or 24 and 48 hours of hypoxia (1% oxygen). For each time point and condition was performed in duplicate was produced Total RNAs of six samples were extracted and analysed.

2016-08-25 | E-GEOD-76739 | biostudies-arrayexpress

Implication of Long noncoding RNAs in the endothelial cell response to hypoxia revealed by RNA-sequencing.

Project description:Long noncoding RNAs (lncRNAs) are non-protein coding RNAs regulating gene expression. Although for some lncRNAs a relevant role in hypoxic endothelium has been shown, the regulation and function of lncRNAs is still largely unknown in the vascular physio-pathology. Taking advantage of next-generation sequencing techniques, transcriptomic changes induced by endothelial cell exposure to hypoxia were investigated. Paired-end sequencing of polyadenylated RNA derived from human umbilical vein endothelial cells (HUVECs) exposed to 1% O2 or normoxia was performed. Bioinformatics analysis identified â 2000 differentially expressed genes, including 122 lncRNAs. Extensive validation was performed by both microarray and qPCR. Among the validated lncRNAs, H19, MIR210HG, MEG9, MALAT1 and MIR22HG were also induced in a mouse model of hindlimb ischemia. To test the functional relevance of lncRNAs in endothelial cells, knockdown of H19 expression was performed. H19 inhibition decreased HUVEC growth, inducing their accumulation in G1 phase of the cell cycle; accordingly, p21 (CDKN1A) expression was increased. Additionally, H19 knockdown also diminished HUVEC ability to form capillary like structures when plated on matrigel. In conclusion, a high-confidence signature of lncRNAs modulated by hypoxia in HUVEC was identified and a significant impact of H19 lncRNA was shown Total RNA was extracted from two independent experiments with different time-points of hypoxia exposure (1% oxygen). HUVEC were exposed to 24h normoxia and 24h hypoxia or to 24h normoxia and 48h hypoxia. Each experiment was performed in duplicate.

2016-08-25 | E-GEOD-76743 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data