Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mus musculus

ABSTRACT: High-resolution Sox2 DNA-binding sites mapping by ChIP-exo in TSA-treated ES cells

PROVIDER: PRJNA266322 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1640066.fastq.gz	Fastqsanger.gz

Items per page:

1 - 1 of 1

Similar Datasets

Mus musculus

Project description:High-resolution Brachyury DNA-binding Sites Mapping by ChIP-exo

| PRJNA238170 | ENA

Single-molecule Dynamics of Enhanceosome Assembly In Embryonic Stem Cells

Project description: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.

2014-03-12 | E-GEOD-54103 | biostudies-arrayexpress

High-resolution Sox2 DNA-binding sites mapping by ChIP-exo in TSA-treated ES cells

Project description:Mapping ultra-high resolution of Sox2:DNA interaction after trichostatin A (TSA) treatment would provide us with valuable new mechanistic insights into how epigenome regulates transcription factor DNA interactions in the cells.

2014-12-01 | GSE62972 | GEO

Data Exploration, Quality Control and Statistical Analysis of ChIP-exo/nexus Experiments

Project description:ChIP-exo/nexus experiments present modifications on the commonly used ChIP-seq protocol for high resolution mapping of transcription factor binding sites. Although many aspects of the ChIP-exo data analysis are similar to those of ChIP-seq, these high throughput experiments pose a number of unique quality control and analysis challenges. We develop a statistical quality control pipeline and accompanying R package, ChIPexoQual, to enable exploration and analysis of ChIP-exo and related experiments. ChIPexoQual evaluates a number of key issues including strand imbalance, library complexity, and signal enrichment of data. Assessment of these features are facilitated through diagnostic plots and summary statistics calculated over regions of the genome with varying levels of coverage. We evaluated our QC pipeline with both large collections of public ChIP-exo/nexus data and multiple, new ChIP-exo datasets from E. coli. ChIPexoQual analysis of these datasets resulted in guidelines for using these QC metrics across a wide range of sequencing depths and provided further insights for modelling ChIP-exo data. Finally, although ChIP-exo experiments have been compared to ChIP-seq experiments with single-end (SE) sequencing, we provide, for the first time, comparisons with paired-end (PE) ChIP-seq experiments. We illustrate that, at fixed sequencing depths, ChIP-exo provides higher sensitivity, specificity, and spatial resolution than PE ChIP-seq and both significantly outperform their SE ChIP-seq counterpart.

2017-03-01 | GSE84830 | GEO

Dynamics of Sox2 occupancy during the differentiation of embryonic stem cells into trophoblast stem cells.

Project description:To understand the mechanism underlying the versatility in transcriptional regulation by Sox2, we compared genome-wide binding sites of Sox2 in embryonic stem (ES) cells and trophoblast stem (TS) cells by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). A tetracycline-inducible Oct3/4 knockout ES cell line ZHBTc4 was treated with Tet for 4 days in the presence of FGF4 and mouse embryonic fibroblasts (MEFs).

2013-10-17 | E-GEOD-28453 | biostudies-arrayexpress

Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems

Project description:Using ChIP-exo, we have identified at single nucleotide resolution genomic binding sites for UvrY in E. coli and its homolog SirA in S. Typhimurium.

2016-10-31 | GSE74810 | GEO

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 | biostudies-arrayexpress

Mapping ONECUT1 TF binding with ChIP-exo

Project description:Mapping ONECUT1 TF binding with ChIP-exo

| PRJEB4933 | ENA

A simple method for generating high-resolution maps of genome wide protein binding

Project description:Chromatin immunoprecipitation (ChIP) and its derivatives are the main techniques used to determine transcription factor binding sites. However, conventional ChIP with sequencing (ChIP-seq) has problems with poor resolution and newer techniques require significant experimental alterations and complex bioinformatics. Here we build upon our high-resolution crosslinking ChIP-seq (X-ChIP-seq) method and compare it to existing methodologies. By using micrococcal nuclease, which has both endo- and exo-nuclease activity to fragment the chromatin and thereby generate precise protein-DNA footprints, high-resolution X-ChIP-seq achieves single base pair resolution of transcription factor binding. A significant advantage of this protocol is the minimal alteration to the conventional ChIP-seq workflow and simple bioinformatic processing. Using High-resolution X-ChIP-seq we determined the genome-wide binding profile of various DNA binding proteins.

2015-06-12 | E-GEOD-67454 | biostudies-arrayexpress

Dynamics of Sox2 and Esrrb occupancy during the differentiation of embryonic stem cells into trophoblast stem cells.

Project description:To understand the mechanism underlying the versatility in transcriptional regulation by Sox2 and Esrrb, we compared genome-wide binding sites of Sox2 and Esrrb in embryonic stem (ES) cells and trophoblast stem (TS) cells by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq).

2013-10-17 | GSE28453 | GEO

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