Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Actively translating transcriptome (Ribotag) profiling of mouse retinal endothelial cells during postnatal development

ABSTRACT: Angiogenesis, a process mediating the expansion of vascular beds in many physiological and pathological settings, requires dynamic changes in endothelial cell (EC) behavior. The molecular mechanisms governing EC activity during different phases of vascular growth, remodeling, maturation, and quiescence remain elusive. Here, we have employed actively translating transcriptome analysis of mouse retinal ECs for the characterization of dynamic gene expression changes during postnatal development and the identification of critical angiogenic factors.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Mus musculus

SUBMITTER: Hyun-Woo Jeong

PROVIDER: E-MTAB-5087 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-Seq Analysis of mouse endothelial cells from multiple organs

Project description:In order to identify the orgnaotypic characteristics of endothelial cells from adipose tissues compared to other organs, we isolated endothelial cells from various organs using the Ribo-Tag method, which tags the ribosomal subunit with hemagglutinin (HA) in VE-Cadherin expressing cells.

2019-12-01 | E-MTAB-6161 | biostudies-arrayexpress

A single cell transcriptome atlas of murine endothelial cells

Project description:The heterogeneity of endothelial cells (ECs), lining blood vessels, across tissues remains incompletely inventoried. We constructed an atlas of >32,000 single-EC transcriptomic data from 11 tissues of the model organism Mus musculus. We propose a new classification of EC phenotypes based on transcriptome signatures and inferred putative biological features. We identified top-ranking markers for ECs from each tissue. ECs from different vascular beds (arteries, capillaries, veins, lymphatics) resembled each other across tissues, but only arterial, venous and lymphatic (not capillary) ECs shared markers, illustrating a greater heterogeneity of capillary ECs. We identified high-endothelial-venule and lacteal-like ECs in the intestines, and angiogenic ECs in healthy tissues. Metabolic transcriptomes of ECs differed amongst spleen, lung, liver, brain and testis, while being similar for kidney, heart, muscle and intestines. Within tissues, metabolic gene expression was heterogeneous amongst ECs from different vascular beds, altogether highlighting large EC heterogeneity.

2020-02-13 | E-MTAB-8077 | biostudies-arrayexpress

The Role of microRNAs in Neural Stem Cell-supported Endothelial Morphogenesis

Project description:MicroRNA microarrays and RNA expression arrays were used to identify functional signaling between neural stem cell progenitor cells (NSPC) and brain endothelial cells (EC) that are critical during embryonic development and tissue repair following brain injury. Mouse neural stem /progenitor cells (NSPC) and brain endothelial cells (EC) were co-cultured to identify changes in gene and miRNA profiles induced in ECs under the influence of NSPCs

2011-08-31 | E-GEOD-29759 | biostudies-arrayexpress

Role of microRNAs in Neural Stem Cell-supported Endothelial Morphogenesis

Project description:We checked whether the inhibition of the FGF, VEGF, and TGF signaling pathways would influence the miRNA profile in ECs, co-cultured with NSPCs. EC/NSPC co-cultures were incubated with FGF/VEGF receptor inhibitor PD 173074 (1μM in DMSO), and the TGF-β receptor inhibitor SB431542 (10μM in DMSO, Millipore)

2012-01-01 | E-GEOD-32352 | biostudies-arrayexpress

Gene expression profiling of endothelial cells derived from Foxo1(+/+) and Foxo1(-/-) ES cells in response to VEGF

Project description:VEGF induces elongation of endothelial cells (ECs) that are derived from wild-type (Foxo1(+/+)) ES cells. VEGF-induced EC elongation is an important process of angiogenesis. ECs derived from Foxo1(-/-) ES cells fail to elongate in response to VEGF. Gene expression profiling of wild-type and Foxo1(-/-) ECs in the presence or absence of VEGF stimulation identifies responsible genes that regulate EC elongation. One wild-type (Foxo1(+/+)) ES cell clone and one Foxo1(-/-) ES cell clone were used. ES cells were cultured on OP9 stromal cell layer in the presence or absence of VEGF (10 ng/ml). After 6.5 days, VE-cadherin+ CD31+ ECs were isolated by FACS and used for total RNA extraction. Three independent experiments were performed for each condition.

2016-02-16 | E-GEOD-76366 | biostudies-arrayexpress

Proteomics study in somatic embryogenesis in avocado

Project description:To understand the molecular foundation of the SE induction and development in avocado, we compared by proteomics approach, the embryogenic (EC) and non-embryogenic (NEC) cultures of two avocado varieties. Although Criollo and Hass EC exhibits particularities in the proteome and metabolome profile, in general, we observed a more active phenylpropanoid pathway in EC than NEC. Our proteomic pipeline consisted of a peptide labeled with TMT6plex and synchronous precursor selection (SPS) MS3

2020-08-14 | PXD019705 | Pride

L1CAM overexpression in mouse lung endothelial cells (lECs)

Project description:In an attempt to elucidate the molecular mechanisms underlying the multiple roles of L1 in endothelium, we checked whether manipulating its expression affected the transcriptome of lECs. To this purpose, we compared the gene expression profiles of L1-overexpressing and control lECs by Affymetrix, which revealed a remarkable effect of L1 overexpression on lECs transcriptome. Mouse lung-derived EC (lECs), kindly provided by E. Dejana (Milan, Italy), were stably transfected with a pcDNA3.1/Hygro(-) vector containing mouse LICAM full length or with and empty pcDNA3.1/Hygro(-) vector as control. Three independent experimental replicates were performed.

2014-10-21 | E-GEOD-45859 | biostudies-arrayexpress

The deubiquitinase USP7 stabilizes Maf proteins to promote myeloma cell survival

Project description:USP7, as a deubiquitination enzyme, controls ubiquitination and stability of Maf family proteins. USP7 promotes Maf transcriptional activity. Moreover, USP7 is overexpressed in multiple myeloma cells and its expression level is negatively correlated to the survival of myeloma patients.

2019-12-16 | PXD016020 | Pride

Endothelial cell heterogeneity in pathological angiogenesis characterized by metabolic transcriptome diversity

Project description:Endothelial cell (EC) metabolism is an emerging target for anti-angiogenic therapy in tumor and choroidal neovascularization (CNV), but little is known about individual EC metabolic transcrip-tomes. Here, by scRNA-sequencing 28,337 murine choroidal ECs (CECs) and sprouting CNV-ECs, we constructed a taxonomy to characterize their heterogeneity. Comparison with murine lung tumor ECs (TECs) revealed congruent marker gene expression by distinct EC phenotypes across tissues and diseases, suggesting similar angiogenic mechanisms. Trajectory inference of CNV-ECs revealed that differentiation of venous to angiogenic ECs was accompanied by metabolic transcriptome plasticity. EC phenotypes displayed metabolic transcriptome heterogeneity. Hypothesizing that conserved genes are more important, we used an integrated analysis, based on congruent transcriptome analysis, CEC-tailored genome scale metabolic modeling, and gene expression me-ta-analysis in multiple cross-species datasets, followed by functional validation, to identify the top-ranking metabolic targets SQLE and ALDH18A1, involved in EC proliferation and collagen production, respectively, as novel angiogenic targets.

2020-03-31 | E-MTAB-8604 | biostudies-arrayexpress

Sheared HUVEC conditioned media nano-LC MSMS

Project description:Primary human umbilical vein endothelial cells (HUVECs, n=4) were exposed to low-magnitude pre-conditioning FSS (1.5 dynes/cm2) 18h using the Ibidi pump system followed by exposure to the arterial- (15 dynes/cm2) or venous-magnitude (1.5 dynes/cm2) FSS for 24h. Conditioned media was collected to analyse the effect of acute changes in the haemodynamic environment on the EC secretome.

2024-07-15 | PXD050737 | Pride

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