Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

41 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bacterial cellulose carrier maintains native endothelial cell differentiation in vitro

ABSTRACT: A comprehensive transcriptomic and proteomic characterization of native HUVEC and HUVEC grown on collagen-coated Xellulin and collagen-coated conventional cell culture plastic from six donors, a total of 28 samples/libraries in 3 groups (1) Native HUVEC freshly isolated from six umbilical cords and then propagated (passage 0) (2) Ten samples of HUVEC passage 1 cultured on Xell-Discs Xellulin (3) twelve samples HUVEC passage 1 cultured in standard plastic cell culture

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Lukas Jost

PROVIDER: E-MTAB-4747 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of Homo Sapiens Human Umbilical Endothelial Cells normal vs treated with TNF to investigate effect of TNF-alpha on microRNAs levels

Project description:Effect of TNF-alpha on microRNAs levels in Human Umbilical Endothelial Cells (HUVECs). HUVEC that were treated or not for 2 or 24 hours with TNF (10 ng/ml). Duplicate samples (1 or 2) of two different isolations of HUVEC (A or B)

2009-12-01 | E-MTAB-150 | biostudies-arrayexpress

Transcription profiling of human umbilical vein endothelial cells during senescence and tBHP treatment

Project description:Identification of differentially expressed genes in HUVEC senescence and tBHP treatment.

2010-07-30 | E-MEXP-2283 | biostudies-arrayexpress

Transcriptome analysis of HUVEC

Project description:Human umbilical vein endothelial cells (HUVEC) were isolated from umbilical cords from four different donors, as previously described (Cooke et al., 1993). Cells were maintained in Medium 199 (M199, Invitrogen) containing 20% fetal calf serum, 28g/ml gentamycin, 2.5g/ml amphotericin B, 1ng/ml epidermal growth factor and 1g/ml hydrocortisone (all from Sigma) for 48 hours prior to processing. HUVEC cultures isolated using this method were 96-98% pure, determined by positive staining by flow cytometry of CD105, CD31 and vWF and the expression of elevated levels of intracellular adhesion molecule (ICAM-1) and E-selectin following stimulation with the inflammatory cytokine interleukin-1. Total HUVEC RNA was isolated using the RNeasy mini kit with QIAshredder (Qiagen) according to the manufacturers instructions. RNA integrity number was >8.0 for all samples.

2016-09-30 | E-MTAB-4897 | biostudies-arrayexpress

KSHV G-protein-coupled receptor (GPCR) induced gene transcription in HUVEC cells

Project description:We used microarrays to compare the gene transcription level between HUVEC-kGPCR and HUVEC-vector stable cells. The goal is to identify the genes that are affected by KSHV kGPCR expression. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. HUVEC cells were infected with kGPCR or control lentivirus and selected with puromycin to get stable cells. Then RNA was extracted from these cells and microarray analysis was performed.

2015-03-05 | E-GEOD-66503 | biostudies-arrayexpress

PDGFR-alpha inhibits melanoma growth via CXCL10/IP-10 and miR-503. A multi-omics approach.

Project description:Cutaneous melanoma is the most aggressive skin cancer showing high mortality at advanced clinical stages. Platelet-Derived Growth Factor Receptor alpha (PDGFR-alpha) is known to strongly inhibit melanoma and endothelial cells proliferation, in vitro as well in vivo. PDGFR-alpha expression has been found to be reduced in metastatic human melanoma-biopsies, as compared to benign nevi-biopsies, thus implying a negative selection of PDGFR-alpha expressing cells, in melanoma. In the present study PDGFR-alpha was transiently overexpressed in endothelial (HUVEC) and melanoma (SK-Mel-28) human cells; a strong anti-proliferation effect was observed, along with profound effects on mRNA and miRNA expression. In detail, gene-expression profiling showed that PDGFR-alpha over-expression affects the expression of 82 transcripts in HUVEC (41 up-, 41 down-regulated), and 52 Transcripts in SK-Mel-28 (43 up-, 9 down-regulated). Finally, a miRNA profiling showed that 14 miRs are up-regulated and 39 are down-regulated in PDGFR-alpha overexpressing cells. Accurate validation with alternative techniques demonstrated that CXCL10 is one of the most significantly up-regulated at both gene- and protein level, in combination with a strong down-regulation of miR-503 in both HUVEC and SK-Mel-28 overexpressing PDGFR-alpha. We then demonstrate that CXCL10 is a validated miR-503 target, and that the anti-proliferation effect of PDGFR-alpha is reverted by specific CXCL-10 neutralization. In conclusion, PDGFR-alpha overexpression strongly inhibits endothelial- and melanoma- proliferation in a CXCL-10 dependent way, by significantly down-regulating miR-503 expression. This data set contains the results of the mRNA analysis.

2016-11-14 | E-MTAB-4261 | biostudies-arrayexpress

Comparison of gene expression between Human umbilical vein endothelial cells and Human liver sinusoidal endothelial cells

Project description:To identify leukocyte adhesion receptors which differentially regulate recruitment in human liver sinusoidal endothelial cells compared to a protoptypic venular endothelium Gene expression was measured in four groups Group 1: cultured human liver sinusoidal endothelial cells (HSEC) Group 2: cultured human umbilical vein endothelial cells (HUVEC) Group3: Interferon gamma and tumour necrosisfactor alpha treated HSEC and Group 4: Interferon gamma and tumour necrosisfactor alpha treated HUVEC. Two replicates were used for each group.

2016-10-24 | E-GEOD-78020 | biostudies-arrayexpress

Global analysis of NFATc1 binding and histone marks in VEGF-activated endothelial cells

Project description:We performed the newly mapping of genome-wide NFATc1 binding events in VEGF-stimulated primary cultured endothelial cells, by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). Combined NFATc1 ChIP-seq profile and the epigenetic histone marks revealed that predominant NFATc1-occupied peaks were overlapped with promoter marking but not silencer marking. DNA microarrays with NFATc1 expression or knockdown indicated the predominant NFATc1 binding targets were correlated with induced patterns. Examination of NFATc1 and two different histone marks in HUVEC in the presence/absense of VEGF.

2013-09-01 | E-GEOD-49428 | biostudies-arrayexpress

Transcriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development [Illumina]

Project description:Long non-coding RNAs (lncRNAs) have emerged as critical regulators of gene expression and chromatin modifications, with important functions in development and disease. Here we sought to identify and functionally characterize lncRNAs critical for vascular vertebrate development with significant conservation across species. Genome-wide transcriptomic analyses during human vascular lineage specification enabled the identification of three conserved novel lncRNAs: TERMINATOR, ALIEN and PUNISHER that are specifically expressed in pluripotent stem cells, mesoderm and endothelial cells, respectively. Gene expression profiling, alongside RNA immunoprecipitation coupled to mass spectrometry, revealed a wide range of new molecular networks and protein interactors related to post-transcriptional modifications for all three lncRNAs. Functional experiments in zebrafish and murine embryos, as well as differentiating human cells, confirmed a developmental-stage specific role for each lncRNA during vertebrate development. The identification and functional characterization of these three novel non-coding provide a comprehensive transcriptomic roadmap and shed new light on the molecular mechanisms underlying human vascular development. shRNA knock down of lncRNAs followed by DNA methylation profiling

2015-05-15 | E-GEOD-54966 | biostudies-arrayexpress

DHA effect on endothelial cells (HUVEC) under proinflammatory condition

Project description:Transcriptional profiling of Human Umbilical Vein Endothelial Cells (HUVEC) comparing untreated control cells with IL-1-treated cells with or without pre-treatment with DHA. Three condition experiment: DHA treated HUVEC cells (25 µmol/L DHA for 48 hours) vs control; IL-1 treated HUVEC cells (5ng/ml for 3 hours) vs control; HUVEC treated with 25 µmol/L DHA for 48 hours and then stimulated with 5 ng/mL IL-1? for 3 hours. For each condition, 3 replicates

2015-05-20 | E-GEOD-57825 | biostudies-arrayexpress

Low- and middle-dose of radiation on hNPC and HUVEC

Project description:Many neural progenitor cells present in the fetus, but also in adult brain, which play a major role for the reproduction for healingin regeneration of neuronal cells, when differentiated cells are damaged. However, effects of radiation effect on undifferentiated neural progenitor cells remained unclear. The radiation doses of medical exposure, pollution by nuclear power plant accidents, and other exposure of workers; medical workers, airline crews, and astronaut have been focused. In this study, we report the effects of low- to middle- dose doses of radiation on cultured human neural progenitor cells (hNPC) differentiated derived from embryonic stem (ES) cells, which are partially compared with those of human umbilical vein endothelial cell (HUVEC). Gene expression was changed by continuous exposure of 31mGy; 0.0072 mGy/ minute, 124mGy; 0.029 mGy/ minute and 496mGy; 0.085 mGy/ minute for seventy-two hours. While shortening in neurite length by 124mGy was not significant, its decrease was observed by 496 mGy of radiation. Number of altered pathways increased dose-dependently. By thirty-one mGy per 72 hours of radiation, gene expression of inflammatory pathways involving interferon and cell junction were changed. By 124 mGy of radiation, DNA double strand break repair pathways and cell adhesion molecules were affected. Then, 496 mGy of radiation for 72 hours altered translational DNA synthesis pathway, apoptotic pathway, various metabolic pathways and neural differentiation pathways. Dose-dependent transcriptional changes by low- to middle- radiation are consistent with gradual axonal shortening, growth arrest and neural cell death. Undifferentiated hNPC derived from embryonic stem (ES) cells and HUVECs synchronized in G1 cell cycle phase were irradiated from sealed cesium-137 for 72 h.

2015-03-31 | E-GEOD-67309 | 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