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

Nucleosome mapping data from GR and cell-cycle regulated genes in human cell lines

ABSTRACT: Human UL3 cells (U20S derivatives containing GR and an MMTV-luc transgene) were treated with dexamethasone for 0, 1 or 4 hrs. Chromatin was harvested, digested with to ~70% mononucleosomes with MNase, and isolated mononucleosome fragments were used to probe custom Nimblegen genomic tiling microarrays. In addition, human HL60 cells were treated with or without DMSO to induce granulocyte differentiaton, and mononucleosome positions mapped. MNase digested bare DNA fragments of ~500 bp average length from UL3 cells was used as a control. Mononucleosome positions at tiled genes for UL3 cells +/- dexamethasone and HL60 cells +/- DMSO.

ORGANISM(S): Homo sapiens

SUBMITTER: Gavin Schnitzler

PROVIDER: E-GEOD-25281 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Multiple distinct stimuli increase measured nucleosome occupancy around human promoters.

Pham Chuong D CD Sims Hillel I HI Archer Trevor K TK Schnitzler Gavin R GR

PloS one 20110811 8

Nucleosomes can block access to transcription factors. Thus the precise localization of nucleosomes relative to transcription start sites and other factor binding sites is expected to be a critical component of transcriptional regulation. Recently developed microarray approaches have allowed the rapid mapping of nucleosome positions over hundreds of kilobases (kb) of human genomic DNA, although these approaches have not yet been widely used to measure chromatin changes associated with changes in ...[more]

PMID: 21853138

Similar Datasets

Mouse Models for Muscular Dystrophy

Project description:Comparative analysis of gene expression levels from hindlimb muscle tissue from 8 week old mouse models for muscular dystrophy. We have used mouse models with dystrophin-, sarcoglycan-, sarcospan-, or dysferlin-deficiency. Keywords = muscular dystrophy

2010-06-06 | E-GEOD-2112 | biostudies-arrayexpress

Schistosoma japonicum gender-associated differentially expressed genes

Project description:Suppression subtractive hybridization(SSH) libraries of Schistosoma japanicum female and male worms were constructed by using Clontech PCR-selectTM cDNA subtraction kit. S.japonicum cDNA microarrays were fabricated using female and male cDNA clones originating from SSH libraries. female-associated and Male-associated differentially expressed gene clones were obtained, Analysis of gender-associated differentially expressed genes helps to determine which genes are important to sexual maturation of schistosome and better understand schistosome biology and host-parasite relationship, facilitate the discovery of novel gene products that could represent targets for the development of new drugs and vaccines to control chitosomiasis. Keywords: gender-associated Four Samples were analyzed about Schistosoma japonicum gender-associated differentially expressed genes

2012-03-05 | E-GEOD-3641 | biostudies-arrayexpress

Time-course of mdx and wild type mice

Project description:Time-course microarray data set of mdx and wild type mice ranging from 1-20 weeks of age Keywords: time-course

2010-05-27 | E-GEOD-1574 | biostudies-arrayexpress

Mouse Inbred Strain Variation Muscle

Project description:Variation in gene expression profiles was determined between mouse inbred strains in hindlimb muscle tissue. Strains under investigation were: C57Bl/6, C57Bl/10, CBA, DBA2, and BALB/c.

2003-12-09 | E-GEOD-662 | biostudies-arrayexpress

Skeletal muscle cell fusion time course

Project description:Time course experiment of healthy primary skeletal muscle cells KM109, KM108 and HPP4 after initiation of fusion This SuperSeries is composed of the following subset Series: GSE884: KM109 GSE895: KM108_cDNA GSE896: HPP4_cDNA

2004-02-11 | E-GEOD-906 | biostudies-arrayexpress

Nucleosome mapping data from GR and cell-cycle regulated genes in human cell lines

Project description:Human UL3 cells (U20S derivatives containing GR and an MMTV-luc transgene) were treated with dexamethasone for 0, 1 or 4 hrs. Chromatin was harvested, digested with to ~70% mononucleosomes with MNase, and isolated mononucleosome fragments were used to probe custom Nimblegen genomic tiling microarrays. In addition, human HL60 cells were treated with or without DMSO to induce granulocyte differentiaton, and mononucleosome positions mapped. MNase digested bare DNA fragments of ~500 bp average length from UL3 cells was used as a control.

2011-08-21 | GSE25281 | GEO

TGF-b signaling and response

Project description:This work evaluates new and specific therapeutic targets and molecular diagnostic markers connected to the TGF-b response system in chronic fibrotic diseases.

2010-06-09 | E-GEOD-579 | biostudies-arrayexpress

Anopheles gambiae immune responses to human and rodent Plasmodium parasite species

Project description:Transmission of malaria is dependent on the successful completion of the Plasmodium lifecycle in the Anopheles vector. Major obstacles are encountered in the midgut tissue, where most parasites are killed by the mosquito’s immune system. In the present study, DNA microarray analyses have been used to compare Anopheles gambiae responses to invasion of the midgut epithelium by the ookinete stage of the human pathogen Plasmodium falciparum and the rodent experimental model pathogen P. berghei. Invasion by P. berghei had a more profound impact on the mosquito transcriptome, including a variety of functional gene classes, while P. falciparum elicited a broader immune response at the gene transcript level. Ingestion of human malaria-infected blood lacking invasive ookinetes also induced a variety of immune genes, including several anti-Plasmodium factors. By comparing gene expression patterns between carcassess or guts of mosquitoes that fed on a P. falciparum or P. berghei wt and mosquitoes that fed on invasion incapable strains we gain information on the A. gambiae transcriptional responses to the invading ookinete at 24 hours after feeding. By comparing gene expression patterns between carcassess or guts of mosquitoes that fed on a P. falciparum ookinete invasion incapable strain and mosquitoes that fed on non-infected blood we gain information on the A. gambiae transcriptional responses to malaria infected blood in absence of ookinete invasion at 24 hours after feeding. By comparing gene expression patterns between mosquitoes at 4 hours after being injected with either E. coli or S. aureus and mosquitoes injected with sterile PBS we gain information on the mosquito's transcriptional response to these bacterial challenges.

2007-08-15 | E-GEOD-8789 | biostudies-arrayexpress

nasopharyngeal carcinoma versus nasopharyngeal phlogistic tissue reference

Project description:Nasopharyngeal carcinoma (NPC) remains a majoy health problem worldwide, specially in Southeast China. In order to find the new candidate genes and molecular markers that are associated with nasopharyngeal carcinoma (NPC), this study focused on the screening NPC relative genes by gene expression profile. Keywords: disease state analysis 23 NPC biopsies and 15 nasopharynx chronic phlogistic biopsies were used to screen NPC relative genes by BioStarH-141s (2004) profile gene chips which contained 14112 points of full length human genes. The tumor samples were labeled with Cy5-dUTP.The nasopharyngeal phlogistic tissues were labeled with Cy3-dUTP. Biostatistics and bioinformatics were also used to analyse the differently expressed genes.

2009-04-21 | E-GEOD-11219 | biostudies-arrayexpress

Fibrosis associated changes detected in the proteome of surface epithelium overlying Crohn’s Disease Strictures

Project description:Background and aims: Intestinal fibrosis is a common complication of Crohn’s disease (CD). It is characterised by an excessive accumulation of fibroblasts differentiating into activated myofibroblasts secreting excessive extracellular matrix. The potential role of the intestinal epithelium in this fibrotic process remains poorly defined. Methods: A total of 113 CD and control subjects were studied. We performed a pilot proteomic study comparing the proteome of surface epithelium isolated by laser capture microdissection in normal and fibrotic zones of resected ileal CD strictures (n=5). Selected proteins were validated by immunohistochemistry (IHC) in colonic and ileal samples of stricturing CD patients (n=44), pure inflammatory CD (n=29) and control subjects (n=40). Functional assays with cell lines cultures and a fibroblast to myofibroblast differentiation model were used to assess the role of the highlighted epithelial proteins in CD fibrosis. Results: Proteomic study revealed an endoplasmic reticulum (ER) stress and unfolded protein response (UPR) markers increase in the epithelium overlying ileal fibrotic strictures, involving Anterior gradient protein 2 homolog (AGR2) and Binding immunoglobulin protein (BiP). This was confirmed by IHC. The ER stress induction in intestinal epithelial cells increased AGR2 as well as BiP expression and led to an extracellular secreted AGR2. A fibroblast to myofibroblast differentiation was obtained with the supernatant of intestinal epithelial cells pre-conditioned by ER stress and with recombinant AGR2. Conclusions: AGR2 and other ER stress markers are increased within the intestinal epithelium overlying fibrotic strictures and might contribute to profibrotic signals involved in CD fibrosis.

2022-04-04 | PXD022214 | 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