Name: Single-molecule Dynamics of Enhanceosome Assembly In Embryonic Stem Cells
Keywords: ChIP-seq

Omics DI

Browse
Submit Data
Database
Help
Login

Dataset Information

165 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-molecule Dynamics of Enhanceosome Assembly In Embryonic Stem Cells

ABSTRACT: These ChIP-exo data were used to validate the predictions from our live-cell single-molecule imaging experiment The ChIP-exo mapping of ultra-fine localization of endogenous Sox2, halo-Sox2, and two halo-Sox2 mutants (halo-Sox2M and halo-Sox2D) in embryonic stem cells.

ORGANISM(S): Mus musculus

SUBMITTER: Zhe Liu Liu Zhe Li Li

PROVIDER: E-GEOD-54103 | ArrayExpress | 2014-03-12

SECONDARY ACCESSION(S): GSE54103SRP035412PRJNA235183

REPOSITORIES: GEO, ArrayExpress, ENA

ACCESS DATA

Json Xml

Similar Datasets

High-resolution Brachyury DNA-binding Sites Mapping by ChIP-exo

Project description:Mapping ultra high resolution of Brachyury:DNA interaction would provide us with valuable new mechanistic insights into complex molecular transactions at Brachyury-bound enhancers. Embryonic stem cells were differentiated into Brachyury-positive mesoendoderm cells. And, ChIP-exo experiment was then performed to identify detailed Brachyury-DNA binding profiles.

2014-03-10 | E-GEOD-54963 | ArrayExpress

High-resolution Sp1 DNA-binding Site Mapping by ChIP-exo in STHdh Q7/Q7 cells

Project description:Mapping ultra-high resolution of Sp1:DNA interaction would provide us with valuable new mechanistic insights into Sp1-mediated gene regulatory network in Huntington Disease cell culture model. STHdh Q7/Q7 cells were directly fixed and used for the ChIP-exo experiment.

2016-07-15 | E-GEOD-84056 | ArrayExpress

ChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w sequenced by SOLiD

Project description:We determined DNA-binding sites of the yeast transcription factor Yfl052w by ChIP-exo. Cells were grown in the YP media containing palatinose. Yfl052w was tagged with HA tag and anti-HA antibody was used for the immunoprecipitation. Examination of Yfl052 trancription factor in HA-tagged and wt cells (as a control)

2014-07-24 | E-GEOD-57901 | ArrayExpress

ChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w sequenced by Illumina

2014-07-24 | E-GEOD-57900 | ArrayExpress

Charting Brachyury-mediated Developmental Pathways During Early Mouse Embryogenesis

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

2014-03-10 | E-GEOD-54985 | ArrayExpress

ChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w

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

2014-07-22 | E-GEOD-57902 | ArrayExpress

Genome-wide binding of GATA1 and TAL1 determined at high resolution

Project description:Erythroid development and differentiation from multiprogenitor cells to red blood cells requires precise transcriptional regulation. Key erythroid transcription factors, GATA1 and TAL1, co-operate, along with other proteins, to regulate many aspects of this process. How GATA1 and TAL1 are positionally organized with respect to each other and their cognate DNA binding site across the mouse genome remains unclear. We applied high resolution ChIP-exo to GATA1 and TAL1 to study their positional organization across the mouse genome during GATA1-dependent maturation. Two complementary methods, MultiGPS and peak-pairing, were used to determine high confidence binding locations by ChIP-exo. We identified ~10,000 GATA1 and ~15,000 TAL1 locations, which were essentially confirmed by ChIP-seq. Of these, ~4,000 locations were bound by both GATA1 and TAL1. About three-quarters of these were tightly linked (<40 bp away) to a partial E-box located 7-8 bp upstream of a WGATAA motif. Both TAL1 and GATA1 generated distinct characteristic ChIP-exo peaks around WGATAA motifs, that reflect on their positional arrangement within a complex. We show that TAL1 and GATA1 form a precisely organized complex at a compound motif consisting of a TG 7-8 bp upstream of a WGATAA motif across thousands of genomic locations. Genome wide analysis of GATA1 and TAL1 in G1E and G1E-ER4 cells using ChIP-exo experiments

2015-09-17 | E-GEOD-68964 | ArrayExpress

Transcription factor binding in liver tissue isolated from WT and GRdim mice

Project description:We report ChIP-seq and ChIP-exo data for GR in liver tissue isolated from WT and GRdim mice. Comparison of the mouse models reveals that GR interacts with the genome as both a monomer and dimer. Examination of GR, RNAPII and CEBPb binding in WT and GRdim mice on a genome-wide scale

2015-04-14 | E-GEOD-59752 | ArrayExpress

Zygotic gene activatory network in zebrafish is globally controlled by Pou5f1 SoxB1 enhancers

Project description:Genetic control of pluripotent mammalian ES cells is determined by a transcriptional network, with a "central core" of transcription factors, Pou5f1, Sox2 and Nanog. Zebrafish homologues of the "core pluripotency factors" Pou5f1, SoxB1 and Nanog-like are also crucially involved in early development. However, the degree of functional similarity of the network between mammals and non-mammals is a matter of debate. To identify the components of Pou5f1-dependent transcriptional networks, we determined the genomic binding sites for Pou5f1 and Sox2 in late blastula stage zebrafish embryos using ChIP-seq. We found that Sox2 and Pou5f1 are co-binding to the regulatory regions of Sox2, Pou5f1, and Nanog-like, as well as to multiple orthologues of mammalian plutipotency network components. Deep sequencing was performed using the Illumina GAIIx on DNA samples obtained from Sox2 ChIP, Pou5f1-Flag ChIP and Input Control. Pou5f1 was analysed in technical duplicates to obtain higher sequencing depth.

2013-08-10 | E-GEOD-39780 | ArrayExpress

Glucocorticoid receptor profiling in IMR90, K562 and U2OS (ChIP-exo)

Project description:To identify the sequences responsible for recruitment of Glucocorticoid receptor (GR) to individual loci, we performed ChIP-seq and ChIP-exo that combines chromatin immunoprecipitation with an exonuclease digestion step. We performed these experiments in three cell lines : IMR90 (ATTC:CCL-186), U2OS osteosarcoma cell lines, K562 (ATCC:CCL243), upon glucocorticoid treatment.

2015-02-25 | E-MTAB-2956 | ArrayExpress

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
GPMDB

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS

ArrayExpress
ExpressionAtlas

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data