Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin immunopreciptiation of liver from wild type and Foxa2 knock out mice to identify Foxa2 binding sites

ABSTRACT: In order to identify the subset of genes directly regulated by Foxa2 in the liver, we performed genome-wide location analysis. Chromatin immunoprecipitation (ChIP) samples from livers of wild type and Foxa2 liver-conditional null mice (Foxa2loxP/loxPAlfp.Cre) were hybridized to a mouse enhancer/promoter microarray with more than 36,000 elements (BCBCPromChip 5). This analysis identified 574 enhancer and promoter regions, corresponding to 484 unique genes, as occupied by Foxa2 in the adult liver.

ORGANISM(S): Mus musculus

SUBMITTER: Irina Bochkis

PROVIDER: E-MEXP-1675 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Chromatin immunoprecipitation of wild type and Foxa2 knock-out mouse liver using anti-HNF6 anitbodies to test whether Foxa2 inhibits HNF6-mediated transcription in the liver

Project description:The aim of this study was to test, in vivo, if Foxa2 inhibits HNF6-mediated transcription in the liver. We utilized hepatocyte-specific gene ablation of Foxa2 and the Mouse PromoterChip BCBC 3.0 and Mouse PancChip 5.0 cDNA microarrays to investigate HNF6 binding to its target promoters in vivo in the presence or absence of Foxa2. For the mouse promoter microarray analysis, chromatin immunoprecipitation using anti-HNF6 antibodies was performed on chromatin isolated from Foxa2loxP/loxP Alfp.Cre and control mouse livers. Along with sheared genomic DNA (common reference), the immunoprecipitated DNA was amplified, labeled and hybridized to the Mouse PromoterChip BCBC 3.0. For microarray analysis of gene expression, liver RNAs were isolated from three Foxa2loxP/loxP Alfp.Cre and three control mice. RNAs were reverse transcribed, labeled, and hybridized to the Mouse PancChip 5.0. Overall, our studies demonstrate that HNF6 binds to and regulates its target promoters in vivo in the presence and absence of Foxa2 and that the expression levels of HNF6 targets are not influenced by Foxa2.

2007-09-14 | E-CBIL-36 | biostudies-arrayexpress

Chromatin immunoprecipitation of mouse liver to identify the genome wide location of Foxa2 binding

Project description:Genome wide location analysis of Foxa2 in the liver using Agilent Mouse Promoter ChIP-on-Chip Microarray

2009-05-08 | E-MEXP-2111 | biostudies-arrayexpress

Chromatin immunoprecipitation of adult mouse liver to identify Foxa2 targets

Project description:We performed genome-wide location analysis for Foxa2 to identify its targets in the adult mouse liver. Chromatin isolated from the liver of five adult mice was cross-linked, sheared and immunoprecipitated with a Foxa2-specific antibody. The resulting material, as well as material that was not immunoprecipitated, was uncross-linked, amplified, labeled and hybridized to the Mouse Promoter Chip BCBC-5A. Statistical analysis resulted in a set of 107 genes that are bound by Foxa2. Using computational analyses, we showed that Foxa2 containing cis-regulatory modules are dependent on the strength of the Foxa2 consensus site present.

2008-07-04 | E-MTAB-32 | biostudies-arrayexpress

Transcription profiling of wild type and Foxa2 knock out mouse mature beta cells

Project description:The winged helix transcription factor Foxa2 regulates Pdx1 gene expression and fetal endocrine pancreas development. We show here by inducible gene ablation that Foxa2 inactivation in mature beta-cells induces hyperinsulinemic hypoglycemia in Foxa2loxP/loxP, Pdx1-CreERT2 adult mice. Mutant beta-cells exhibited a markedly increased pool of docked insulin granules, some of which were engaged in sequential or compound exocytosis, consistent with an increased first phase glucose-stimulated insulin secretion. Expression of multiple genes involved in vesicular trafficking, membrane targeting and fuel-secretion pathways is dependent on Foxa2. In addition, impaired cytosolic Ca2+ oscillations and elevated intracellular cAMP production accompanied this secretory defect, and were likely contributors to the sensitization of the exocytotic machinery. Thus, in the absence of Foxa2, alterations in intracellular second messenger signaling redistribute the insulin granules into the readily releasable pool. We conclude that Foxa2 is required both for the fetal pancreas development and for the function of mature beta-cells.

2007-09-22 | E-CBIL-39 | biostudies-arrayexpress

Transcription profiling of mouse liver from wild type and Foxa2 knock out strains fed on standard diet

Project description:Transcriptional profiling of changes in global hepatic gene expression in mice lacking Foxa2 in the liver (Foxa2loxP/loxP;Alfp.Cre) on standard rodent diet<br><br><br><br>

2009-05-01 | E-MEXP-2106 | biostudies-arrayexpress

Transcription profiling of mouse liver from wild type and Foxa2 knock out strains fed on a diet supplemented with cholic acid

Project description:Transcriptional profiling of changes in global hepatic gene expression in mice lacking Foxa2 in the liver (Foxa2loxP/loxP;Alfp.Cre) on a diet supplemented with cholic acid, a naturally occurring bile acid

2009-05-08 | E-MEXP-2107 | biostudies-arrayexpress

ChIP-Chip and SACO Analysis of Pdx-1 binding in NIT-1 Insulinoma Cells

Project description:The BCBC Promoter Chip 5B was used to identify genomic targets of Pdx-1 binding. Genomic DNA from mouse NIT-1 insulinoma cells was immunoprecipitated with a Pdx-1 Antibody, PCR amplified, and labeled to the chip. All hybridizations were versus a common reference sample which was a labeled IgG IP. Additionally a Pdx1 SACO library for NIT-1 cells was generated.

2014-11-21 | E-MTAB-3126 | biostudies-arrayexpress

T1E PS28 vs T1E PS28 Indole

Project description:Transcriptional profile of Pseudomonas putida DOT-T1E PS28 grown in the presence of indole (300 uM) compared with the same cells grown in absence of indole.

2013-03-15 | E-MEXP-3825 | biostudies-arrayexpress

T1E-18 vs T1E-18 Ampicillin

Project description:Transcriptional profile of Pseudomonas putida DOT-T1E-18 grown in the presence of ampicillin (100 ug/ml) compared with the same cells grown in absence of ampicillin.

2013-03-15 | E-MEXP-3824 | biostudies-arrayexpress

T1E vs T1E Ampicillin

Project description:Transcriptional profile of Pseudomonas putida DOT-T1E grown in the presence of ampicillin (300 ug/ml) compared with the same cells grown in absence of ampicillin

2013-03-15 | E-MEXP-3823 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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