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

Chromatin immunoprecipitation of mouse MIN6 pancreatic beta cells to identify Pdx1 targets

ABSTRACT: The aim of this experiment was to use highthroughput chromatin immunoprecipitation followed by hybridization to promoter microarrays to obtain a comprehensive list of sites in the genome that are physically occupied by Pdx1. Chromatin was prepared from Min6 insulinoma cells and immunoprecipitated with Pdx1 or control antiserum. The precipitated chromatin was then purified, amplified and directly sequenced using Illumina technology.

ORGANISM(S): Mus musculus

SUBMITTER: Mira Sachdeva

PROVIDER: E-MTAB-134 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Pdx1 (MODY4) regulates pancreatic beta cell susceptibility to ER stress.

Sachdeva Mira M MM Claiborn Kathryn C KC Khoo Cynthia C Yang Juxiang J Groff David N DN Mirmira Raghavendra G RG Stoffers Doris A DA

Proceedings of the National Academy of Sciences of the United States of America 20091023 45

Type 2 diabetes mellitus (T2DM) results from pancreatic beta cell failure in the setting of insulin resistance. Heterozygous mutations in the gene encoding the beta cell transcription factor pancreatic duodenal homeobox 1 (Pdx1) are associated with both T2DM and maturity onset diabetes of the young (MODY4), and low levels of Pdx1 accompany beta cell dysfunction in experimental models of glucotoxicity and diabetes. Here, we find that Pdx1 is required for compensatory beta cell mass expansion in r ...[more]

PMID: 19855005

Similar Datasets

S2-DRSC Replication Origins

Project description:modENCODE_submission_710 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Early origins of replication were identified by treating cells with hydroxyurea (HU), a potent inhibitor of nucleotide synthesis, in the presence of the nucleotide analogue BrdU. Treatment of synchronized S2-DRSC cells with HU stalls replication forks and activates the intra S-phase checkpoint, thereby limiting BrdU incorporation to those sequences immediately adjacent to early activating replication origins. BrdU enriched sequences surrounding early origins of replication are then enriched by immunoprecipitation with an anti-BrdU antibody. Early origins are then detected by hybridization to Agilent genomic tiling arrays. Peaks are called using MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Keywords: CHIP-chip For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Sex: Male NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Cell Line S2-DRSC

2010-05-15 | E-GEOD-17286 | biostudies-arrayexpress

Kc167 Replication Origins

Project description:modENCODE_submission_709 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Early origins of replication were identified by treating cells with hydroxyurea (HU), a potent inhibitor of nucleotide synthesis, in the presence of the nucleotide analogue BrdU. Treatment of synchronized Kc167 cells with HU stalls replication forks and activates the intra S-phase checkpoint, thereby limiting BrdU incorporation to those sequences immediately adjacent to early activating replication origins. BrdU enriched sequences surrounding early origins of replication are then enriched by immunoprecipitation with an anti-BrdU antibody. Early origins are then detected by hybridization to Agilent genomic tiling arrays. Peaks are called using MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Keywords: CHIP-chip For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Genotype: se/e; Sex: Female NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Cell Line Kc167

2010-05-15 | E-GEOD-17285 | biostudies-arrayexpress

Kc167 Replication Timing

Project description:modENCODE_submission_668 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The relative time of replication for all unique sequences in the Drosophila genome was determined by synchronizing tissue culture cell and differentially labeling early and late replicating intermediates. The differentially labeled replication intermediates were then hybridized to Agilent genomic tiling arrays to identify early and late replicating domains. Keywords: CHIP-chip For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Genotype: se/e; Sex: Female NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Cell Line Kc167

2009-07-29 | E-GEOD-17279 | biostudies-arrayexpress

ML-DmBG3-c2 Replication Timing

Project description:modENCODE_submission_670 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The relative time of replication for all unique sequences in the Drosophila genome was determined by synchronizing tissue culture cell and differentially labeling early and late replicating intermediates. The differentially labeled replication intermediates were then hybridized to Agilent genomic tiling arrays to identify early and late replicating domains. Keywords: CHIP-chip For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Genotype: y v f mal; Sex: Unknown NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2

2009-07-29 | E-GEOD-17281 | biostudies-arrayexpress

S2-DSRC Replication Timing

Project description:modENCODE_submission_669 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The relative time of replication for all unique sequences in the Drosophila genome was determined by synchronizing tissue culture cell and differentially labeling early and late replicating intermediates. The differentially labeled replication intermediates were then hybridized to Agilent genomic tiling arrays to identify early and late replicating domains. Keywords: CHIP-chip For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Sex: Male NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Cell Line S2-DRSC

2010-05-15 | E-GEOD-17280 | biostudies-arrayexpress

Early Origins Meta-peak generation

Project description:modENCODE_submission_3441 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes. These experiments will be conducted in multiple cell types and developmental tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Output file represents the union of the coordinates of peak data from various experiments peak calls. These unioned areas, referred to as meta-peaks, cover any genomic coordinate that has been experimentally shown to be capable of sustaining a peak.

2011-03-16 | E-GEOD-27981 | biostudies-arrayexpress

Chromatin immunoprecipitation of human lymphoblastic cell line GM06990 using anti Histone H3K4me1, H3K4me2, H3K4me3, H3ac and H4ac antibodies using an ENCODE array

Project description:ENCODE ChIP/chip study using lymphoblastic cell line GM06990 and anti Histone H3K4me1, H3K4me2, H3K4me3, H3ac and H4ac antibodies.

2005-06-13 | E-MEXP-269 | biostudies-arrayexpress

Cse4 ChIP-chip

Project description:In order to take an unbiased approach and discover all the locations of Cse4 in the genome, we utilized formaldehyde crosslinking and immunoprecipitation followed by hybridization to DNA microarrays. We analyzed the location of Cse4 in three different strains; one in which the endogenous Cse4 is tagged with 12Myc epitopes (Cse4-12Myc), and one which contained both the endogenous Cse4 (untagged) and an ectopic copy of Cse4-12Myc expressed from the GAL1-10 promoter (pGAL1-10-Cse4-12Myc), and one in which Cse4 is tagged with 3HA epitopes (Cse4-3HA). ChIP-chip was performed using custom microarrays, to look at the genome-wide localization of the centromeric histone variant Cse4. Biological replicates were performed for each Cse4 epitope-tagged strain

2009-08-28 | E-GEOD-17481 | biostudies-arrayexpress

The evolutionary impact of Intragenic FliA Promoters

Project description:We compared RNA levels in wild-type Salmonella enterica serovar Typhimurium with RNA levels in a mutant strain in which the fliA gene was deleted.

2017-09-18 | E-MTAB-6048 | biostudies-arrayexpress

RNA-seq of MG1655 wt and MG1655 delta-phoB strains grown in MOPS media with low phosphate (0.2 mM)

Project description:We used RNA-seq to determine differences in RNA levels between wild-type E. coli K-12 and a ΔphoB mutant, each grown in MOPS media with low phosphate (0.2 mM).

2020-07-12 | E-MTAB-9292 | 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