Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

37 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from vehicle and adrenomedullin treated human lymphatic endothelial cells

ABSTRACT: Human dermal lymphatic endothelial cells were cultured and treated with either vehicle or 10 nM AM for 15 minutes, 1 hour, or 24 hours to assess gene expression changes across the human genome with AM treatment. Two variable experiment, time (0.25, 1, 24 hours) and treament (vehicle vs adrenomedullin) of gene expression in human lymphatic endothelial cells. Biological replicates: 3-4 per condition.

ORGANISM(S): Homo sapiens

SUBMITTER: Kathleen Caron

PROVIDER: E-GEOD-59938 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

DNA methylation regulates lineage-specifying genes in the human vascular system [expression array].

Project description:During embryonic development, the lymphatic system emerges by transdifferentiation from the cardinal vein. Although lymphatic and blood vasculature share a close molecular and developmental relationship, they display distinct features and functions. However, even after terminal differentiation, transitions between the two endothelial cell types have been reported. Since changes in phenotypic plasticity and cellular differentiation processes frequently involve epigenetic mechanisms, we wondered whether DNA methylation might play a role in regulating cell type-specific expression in endothelial cells. By analyzing global gene expression and methylation patterns of primary human dermal lymphatic and blood endothelial cells, we identified a highly significant set of genes, which were differentially methylated and expressed. Pathway analyses of the differentially methylated and upregulated genes in lymphatic endothelial cells revealed involvement in developmental and transdifferentiation processes. We further identified a set of novel genes, which might be implicated in regulating BEC-LEC plasticity and could serve as therapeutic targets and/or biomarkers in vascular diseases associated with alterations in the endothelial phenotype. Expression profile of 10 lymphatic endothelial cells was compared to that of 6 blood endothelial cells, no replicates, no control samples.

2012-04-09 | E-GEOD-32709 | biostudies-arrayexpress

Collaborative Cross founder strain lung miRNA expression after allergen challenge

Project description:The goal of this project was to identify strain-dependent expression of miRNAs in lung tissue from Collaborative Cross founder strains that were sensitized and challenged with house dust mite allergen (Der p 1). We analyzed whole lung RNAs from the eight Collaborative Cross founder strains (n=4/strain, all males) using Affymetrix miRNA 2.0 arrays

2015-03-01 | E-GEOD-63954 | biostudies-arrayexpress

Genome-wide expression analysis of the effects of a parasitic nematode's secreted exosomes on mammalian cells.

Project description:We show that a gastrointestinal nematode that infects mice, Heligmosomoides polygyrus, secretes vesicles packaged with specific microRNAs (miRNAs) and Y RNAs as well as a nematode-specific Argonaute protein. The vesicles are of intestinal origin and are enriched for homologs of mammalian proteins found in exosomes, including heat shock proteins, tetraspanins and an ESCORT protein. The nematode-derived vesicles are internalized by mouse intestinal epithelial cells and mediate changes in expression of host genes involved in inflammation and immunity, including the receptor for the alarmin IL33 as well as a key regulator of MAPK signaling, DUSP1. A total of 12 samples were analyzed, from 4 different conditions: medium, exosome-treated, LPS and LPS+exosomes, each with 3 biological replicates. One of the 'medium' replicates was discarded due to outlier behaviour.

2014-12-24 | E-GEOD-55941 | biostudies-arrayexpress

Gene expression analysis of the immortalized human endothelial cell lines HMEC-1 and TIME

Project description:The distinction between lymphatic and blood vessels is biologically fundamental. Two immortalized cell lines, which have been widely used as models for endothelial cells of blood vascular origin, are the human microvascular endothelial cell line-1 (HMEC-1) and the telomerase-immortalized microvascular endothelial cell line (TIME). However, analysis of protein expression by flow cytometry revealed expression of lymphatic markers on these cell lines. Furthermore, functional in vitro leukocyte transmigration assays demonstrated deficiencies in several steps of the leukocyte extravasation cascade. Hence we performed this microarray analysis of the gene expression in HMEC-1 and TIME. We then compare the expression profiles to those of published blood- and lymphatic endothelial cells. Analysis of the gene expression profile of the immortalized human endothelial cell lines HMEC-1 and TIME to be compared to published primary blood- and lymphatic endothelial cells (see supplementary file linked below).

2013-09-11 | E-GEOD-42216 | biostudies-arrayexpress

Cardiac energy dependence on glucose activates metabolic genes controlled by mTOR

Project description:Mice lacking the expression of Acsl1 in the heart (Acsl1H-/-) have impaired cardiac fatty acid oxidation and develop spontaneous cardiac hypertrophy due to increased mTOR activation. To explore how the loss of ACSL1 alters gene expression, we performed a global gene expression analysis on ventricular RNA isolated from Acsl1H-/- and Acsl1flox/flox mice ten weeks after tamoxifen treatment when ACSL1 protein is completely lost and the specific activity of ACSL1 in Acsl1H-/- hearts is reduced 90% Two-condition experiment, cadiac gene expression of Acsl1H-/- vs Acsl1flox/flox mice 10 weeks after tamoxifen treatment. Biological replicates: 3-4 per condition.

2014-09-29 | E-GEOD-51913 | biostudies-arrayexpress

The condition-dependent transcriptome of Bacillus subtilis 168

Project description:Recent studies revealed the unsuspected complexity of the bacterial transcriptome but its systematic analysis across many diverse conditions remains a challenge. Here we report the condition-dependent transcriptome of the prototype strain B. subtilis 168 across 104 conditions reflecting the bacterium's life-styles. This data set composed of 269 tiling array hybridizations allowed to observe ~85% of the annotated CDSs expressed in the higher 30% in at least one hybridization and thus provide an excellent coverage of the transcriptome of this bacterium. In addition to the Genbank annotation 1583 new segments of the chromosome were identified as transcribed and have transcription levels reported in the data matrix. RNA samples prepared from B. subtilis 168 grown under 104 experimental conditions were reverse transcribed, labeled and hybridized to tiling arrays. Most hybridizations were performed in duplicate or triplicate using RNA isolated from independent cultures. All experiments were performed with strain BSB1 which is a tryptophan-prototrophic (trp+) derivative of the 168 trpC2 strain.

2012-03-07 | E-GEOD-27219 | biostudies-arrayexpress

Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions

Project description:We report the condition-dependent transcriptome of S. aureus HG001, a derivative of strain NCTC 8325, by strand-specific tiling array hybridizations. More than 40 experimental conditions were investigated ranging from optimal in vitro growth to interaction with host cells. Analyses included the systematic mapping of transcription units, annotation of non-coding RNAs, the classification of promoters according to their dependency on SigA and SigB, and the prediction of potentially new transcription factor target sites. Antisense RNAs being of particular interest because of the small number of alternative sigma factors used by S. aureus were found to be relatively rare, overlapping only 6% of the annotated coding genes. RNA samples prepared from S. aureus HG001 grown in shake flask or cell culture infection experiments were reverse transcribed, labeled and hybridized to tiling arrays. Hybridizations were performed in triplicate using RNA isolated from independent cultures.

2016-03-08 | E-GEOD-70040 | biostudies-arrayexpress

Activated Notch-induced transcriptional profile modulation in human primary dermal lymphatic endothelial cells

Project description:Human Notch1 intracellular domain (NICD) was overexpressed in human primary lymphatic endothelial cells (LECs) for 10 and 24 hours by adenovirus. A GFP-control adenovirus-infected cells (24hours) and uninfected cells were also analysed as controls. Total RNAs were harvested and subjected to Affymetrix U133A microarray. Human primary lymphatic endothelial cells (LECs) were isolated from human foreskin and cultured and expanded to population passages 5~6. Healthy subconfluent primary LECs were infected with adenovirus expressing human Notch1 intracellular domain (NICD) for 10 or 24 hours. In parallel, LECs were also infected with a GFP-expressing control adenovirus for 24 hours. Uninfected LECs were also used as a negative control in the same experiments

2010-03-20 | E-GEOD-20978 | biostudies-arrayexpress

Expression profile of human lymphatic endothelial cells under static or oscillatory shear stress conditions in the presence or absence of FOXC2

Project description:Lymphatic valves are specialized units regularly distributed along collecting vessels that allow unidirectional forward propulsion of the lymph, and its efficient transport from tissues to the bloodstream. Lymphatic endothelial cells that cover lymphatic valve sinuses are subjected to complex flow patterns, due to recirculation of the lymph during the collecting vessel pumping cycle. They also express high levels of FOXC2 transcription factor. We used microarrays to study the transcriptional networks controlled by FOXC2 in human lymphatic endothelial cells subjected to oscillatory shear stress or cultured under static conditions. Human lymphatic endothelial cells were transfected with control or FOXC2 siRNAs and subjected to 24-hour oscillatory shear stress (1 dyn/cm2; 1/4 Hz) or kept under static conditions as a control. RNA were amplified and hybridized on Affymetrix Human Gene 1.0 ST Arrays. The experiment was run twice independently, using each time a different siRNA to knockdown FOXC2, as previously described (Sabine et al, 2012, Dev Cell).

2015-11-09 | E-GEOD-60152 | biostudies-arrayexpress

Expression data of blood (BVEC) versus lymphatic (LVEC) vascular endothelial silenced for RhoB and VEZF1

Project description:RhoB null mice show decreases in pathological angiogenesis in the ischemic retina and reduces angiogenesis in response to cutaneous wounding, but enhances lymphangiogenesis following both dermal wounding and inflammatory challenge. We used microarrays to link these unique and opposing roles of RhoB in blood versus lymphatic vasculatures to RhoB/VEZF1-mediated gene regulation in primary human blood versus lymphatic endothelial cells. Pure populations of human primary BVECs and LVECs silenced for RhoB or VEZF1 were used for RNA extraction and hybridization on Affymetrix microarrays. We extracted these cells from human male foreskins from at least four individuals and purified them using Dynabeads associated with vascular markers (CD31 and Podoplanin).

2013-10-28 | E-GEOD-51754 | 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