Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

69 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In Vivo Endothelial Cell Heterogeneity

ABSTRACT: Endothelial cells from nine steady state tissues and two regenerating tissues (bone marrow and liver) were intravitally labeld, isolated via flow sorting, and immediately processed for RNA extraction. When of sufficient quality, the RNA was amplified and hybridized. For comparison, Human Emybryonic Stem Cell-derived Endothelial cells (hESC-ECs) were differentiated and isolated based on similarities to the adult mouse counterparts. Endothelial cells were labeled via intravitally labeling of the vascular bed 8 minutes prior to sacrifice with minimally three markers to identify endothelial cells followed by flow sorting.

ORGANISM(S): Homo sapiens

SUBMITTER: Daniel Nolan

PROVIDER: E-GEOD-47067 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene expression analysis of directly converted brown adipocytes (dBAs).

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-08-12 | E-GEOD-56635 | biostudies-arrayexpress

Estrogen Coordinates Translation and Transcription Revealing a Role for NRSF in Human Breast Cancer Cells

Project description:Analysis of estrogen receptor (ER)-positive MCF7 cell total RNA expression and polysome-assiciated RNA expression following treatment with estradiol (E2) and vehicle (etoh). We used expression microarrays to measure polysome association and total RNA abundance in E2 treated MCF7. These data, along with previously published data, show that genes that are upregulated by estrogen treatment are biased towards association with polysomes. MCF7 cells were grown in hormone depleted media for three days before a 1 hour treatment with E2 or 0.1 % ethanol (vehicle). Total RNA was collected using standard methods and polysome-association RNA from the same cells were collected using sucrose gradient fractionation. Both RNA populations were purified, labeled, and hybridized to Affymetrix Human Genest arrays.

2010-05-07 | E-GEOD-18592 | biostudies-arrayexpress

Integrated Genomics of Ovarian Xenograft Tumor Progression and Chemotherapy Response

Project description:Xenograft ovarian tumors are useful model to test therapeutic candidates in vivo. We used microarrays to gain insight into the expression changes during tumor growth and induced by the vitamin D analog, MT19C at multiple time points. SKOV-3 cells were grown in 10% FBS/DMEM before injection into mice. Total RNA was collected using standard methods.

2011-03-01 | E-GEOD-23616 | biostudies-arrayexpress

Adaptation During Ovarian Cancer Metastasis Reveals a Predictive Gene Signature

Project description:We characterized the genetic copy number and expression differences between matched ovarian primary tumors and omental metastases. Differentially expressed genes revealed that metastases proliferate more and are less apoptotic. Differentially expressed genes revealed a predictive expression signature when applied to other gene expression datasets. 18 samples from 9 matched pairs of primary ovarian tumors and metastases from the omentum were collected.

2012-05-31 | E-GEOD-30587 | biostudies-arrayexpress

Expression data from HEK293 cells with or without MIBP1 overexpression

Project description:The transcription factor c-MYC intron binding protein 1 (MIBP1) binds to various genomic regulatory regions, including intron 1 of c-MYC. This factor is highly expressed in post-mitotic neurons in the fetal brain and may be involved in various biological steps, such as neurological and immunological processes. In this study, we globally characterized the transcriptional targets of MIBP1 and proteins that interact with MIBP1. Microarray hybridization followed by Gene Set Enrichment Analysis revealed that genes involved in the pathways downstream of MYC, NF-M-NM-:B, and TGF-M-NM-2 were downregulated when HEK293 cells stably overexpressed MIBP1. In silico transcription factor binding site analysis of the promoter regions of these downregulated genes showed that the NF-M-NM-:B binding site was the most overrepresented. The upregulation of genes known to be in the NF-M-NM-:B pathway after the knockdown of endogenous MIBP1 in HT1080 cells supports the view that MIBP1 is a downregulator of the NF-M-NM-:B pathway. We also confirmed the binding of the MIBP1 to the NF-M-NM-:B site. By immunoprecipitation and mass spectrometry, we detected O-linked M-NM-2-N-acetylglucosamine (O-GlcNAc) transferase (OGT) as a prominent binding partner of MIBP1. Analyses using deletion mutants revealed that a 154-amino acid region of MIBP1 was necessary for its OGT binding and O-GlcNAcylation. A luciferase reporter assay showed that NF-M-NM-:B-responsive expression was repressed by MIBP1, and stronger repression by MIBP1 lacking the 154-amino acid region was observed. Our results indicate that the primary effect of MIBP1 expression is the downregulation of the NF-M-NM-:B pathway, and that this effect is attenuated by O-GlcNAc signaling. Six total samples were analyzed. Three of empty vector transfectant and three of MIBP1 expressing HEK293 cell clones

2012-01-31 | E-GEOD-26420 | biostudies-arrayexpress

Gene Array Analyzer (GAA): Alternative usage of gene arrays to study alternative splicing events (MoGene array)

Project description:The latest version of microarrays released by Affymetrix, the GeneChip Gene 1.0 ST Arrays (gene arrays), are designed in a similar fashion as exon arrays, which enables to identify differentially expressed exons, rather than only the expression level of whole transcripts. Here, we propose an extension, Gene Array Analyzer (GAA), to our previously published Exon Array Analyzer (EAA). GAA enables to analyse gene arrays on exon level and therefore supports to identify alternative splicing with gene arrays. To show the applicability of GAA, we used gene arrays to profile alternative splice events during the development of the heart. Further re-analysis of published gene arrays could show, that some of these splice events reoccur under pathological conditions. The web interface of GAA is user friendly, functional without set up and freely available at http://GAA.mpi-bn.mpg.de. Alternative splicing and gene expression analysis during development of the heart and cardiomyoyte differentiation.

2011-11-28 | E-GEOD-30429 | biostudies-arrayexpress

Global gene expression analysis of fibroblast, dOB, osteoblast, MSC and MSC-OB

Project description:Comparison of each cell mRNA expression pattern. We generated osteoblasts like cell by direct reprogramming technique from human fibroblast. To confirm dOB gene expression pattern similarity to osteoblasts, we analyzed and compared the gene expression profiles of the samples by cDNA microarry. These analysis revealed that dOB are similar to osteoblats in comparative level to MSC-OB. 6 samples.

2015-05-08 | E-GEOD-52817 | biostudies-arrayexpress

Gene expression analysis of directly converted brown adipocytes (dBAs). [human]

Project description:Comparasion of each cell mRNA expression pattern Human fibroblasts were directly converted into brown adipocytes (dBAs) by transducing some transcription factors. To characterize the dBAs more in detail, RNA extracted from the human WAs, human dBAs, and human iPS-derived brown adipocytes (iBAs) were subjected to DNA microarray analysis, and global gene expression profiles of the cells were compared. 6 samples

2015-08-12 | E-GEOD-56633 | biostudies-arrayexpress

Gene expression analysis of directly converted brown adipocytes (dBAs). [mouse]

Project description:Comparasion of each cell mRNA expression pattern Mouse fibroblasts were directly converted into brown adipocytes (dBAs) by transducing some transcription factors. To characterize the dBAs more in detail, RNA extracted from the mouse brown adipose tissue, mouse dBAs, and mouse iPS-derived brown adipocytes (iBAs) were subjected to DNA microarray analysis, and global gene expression profiles of the cells were compared. 3 samples

2015-08-12 | E-GEOD-56634 | biostudies-arrayexpress

Gene Array Analyzer (GAA): Alternative usage of gene arrays to study alternative splicing events

Project description:This SuperSeries is composed of the following subset Series: GSE30429: Gene Array Analyzer (GAA): Alternative usage of gene arrays to study alternative splicing events (MoGene array) GSE32998: Gene Array Analyzer (GAA): Alternative usage of gene arrays to study alternative splicing events (MoEx array) Refer to individual Series

2011-11-28 | E-GEOD-33183 | 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