Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues

ABSTRACT: SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues

PROVIDER: PRJNA783569 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17038000.fastq.gz	Fastqsanger.gz
	SRR17038001.fastq.gz	Fastqsanger.gz
	SRR17038002.fastq.gz	Fastqsanger.gz
	SRR17038003.fastq.gz	Fastqsanger.gz
	SRR17038004.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues

Project description:We have developed SpyChIP, a method that depends on covalent isopeptide bond formation, to identify sites of cell type-specific transcription factor (TF) occupancy in native physiological contexts without tissue dissociation or nuclei sorting. Using SpyChIP, we characterized the genome-wide binding profiles of the Hox protein Ultrabithorax (Ubx) in two non-overlapping domains of the Drosophila haltere imaginal disc, revealing extensive region-specific Ubx-DNA binding events. The application of cell type-specific covalent bond formation to ChIP sets the stage for carrying out many other cell type-specific analyses and genetic manipulations in vivo that were previously unachievable.

2022-06-02 | GSE189554 | GEO

SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues.

Project description:Chromatin immunoprecipitation (ChIP) is an important technique for characterizing protein-DNA binding in vivo. One drawback of ChIP-based techniques is the lack of cell type-specificity when profiling complex tissues. To overcome this limitation, we developed SpyChIP to identify cell type-specific transcription factor (TF) binding sites in native physiological contexts without tissue dissociation or nuclei sorting. SpyChIP takes advantage of a specific covalent isopeptide bond that rapidly forms between the 15-amino acid SpyTag and the 17-kDa protein SpyCatcher. In SpyChIP, the target TF is fused with SpyTag by genome engineering, and an epitope tagged SpyCatcher is expressed in cell populations of interest, where it covalently binds to SpyTag-TF. Cell type-specific ChIP is obtained by immunoprecipitating chromatin prepared from whole tissues using antibodies directed against the epitope-tagged SpyCatcher. Using SpyChIP, we identified the genome-wide binding profiles of the Hox protein Ultrabithorax (Ubx) in two distinct cell types of the Drosophila haltere imaginal disc. Our results revealed extensive region-specific Ubx-DNA binding events, highlighting the significance of cell type-specific ChIP and the limitations of whole-tissue ChIP approaches. Analysis of Ubx::SpyChIP results provided insights into the relationship between chromatin accessibility and Ubx-DNA binding, as well as different mechanisms Ubx employs to regulate its downstream cis-regulatory modules. In addition to SpyChIP, we suggest that SpyTag-SpyCatcher technology, as well as other protein pairs that form covalent isopeptide bonds, will facilitate many additional in vivo applications that were previously impractical.

| S-EPMC9231492 | biostudies-literature

PBAF complex deficiency in melanoma mediates BAF occupancy and transcription factor dynamics

Project description:PBAF complex deficiency in melanoma mediates BAF occupancy and transcription factor dynamics

| PRJNA723186 | ENA

PBAF complex deficiency in melanoma mediates BAF occupancy and transcription factor dynamics (Chromatin)

Project description:PBAF complex deficiency in melanoma mediates BAF occupancy and transcription factor dynamics (Chromatin)

| PRJNA723190 | ENA

Nucleosome occupancy during NuRD complex induction

Project description:Nucleosome occupancy during NuRD complex induction

| PRJEB26866 | ENA

PBAF complex deficiency in melanoma mediates BAF occupancy and transcription factor dynamics (RNA-Seq)

Project description:PBAF complex deficiency in melanoma mediates BAF occupancy and transcription factor dynamics (RNA-Seq)

| PRJNA723192 | ENA

Genomic occupancy of the INO80 complex [II]

Project description:Genomic occupancy of the INO80 complex [II]

| PRJNA421202 | ENA

A reference map of cardiac transcription factor chromatin occupancy identifies dynamic and conserved transcriptional enhancers

Project description:A reference map of cardiac transcription factor chromatin occupancy identifies dynamic and conserved transcriptional enhancers

| PRJNA510592 | ENA

Nucleosome occupancy during NuRD complex induction

Project description:Molecular functions of the Nucleosome Remodeling and Deacetylation (NuRD) complex in the control of gene expression were investigated using an inducible system to direct its assembly in embryonic stem cells. This dataset identifies genome-wide changes in nucleosome positioning at sites of NuRD association.

2018-05-31 | E-MTAB-6807 | biostudies-arrayexpress

RUNX1 transcription factor genome-wide occupancy in EML cells

Project description:We report the application of sequencing technology for high-throughput profiling of RUNX1 transcription factor occupancy in mouse EML cells. RUNX1 antibody was use for chromatin immunoprecipitation followed by high-throughput sequencing to reveal RUNX1 genome occupancy in hematopoietic stem/progenitor cells. Examination of RUNX1 transcription factor occupancy in EML cells.

2014-10-24 | E-GEOD-62596 | 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