Similar studies for GEO DataSets (Select 200236631) - GEO DataSets

Select item 2002366311.

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [4C]

(Submitter supplied) The transcription factor ZNF143 contains seven tandem zinc fingers and is involved in 3D genome construction; however, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes diverse genomic sites and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites and ZNF143 removal narrows the space between CTCF and cohesin. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL20795
7 Samples

Download data: BEDGRAPH

Series

Accession:: GSE236631

ID:: 200236631

PubMed Similar studies

Select item 2002487372.

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL20795
3 Samples

Download data: BROADPEAK, BW

Series

Accession:: GSE248737

ID:: 200248737

PubMed Similar studies

Select item 2002487363.

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry (RNA-Seq)

(Submitter supplied) The transcription factor ZNF143 contains seven tandem zinc fingers and is involved in 3D genome construction; however, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes diverse genomic sites and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites and ZNF143 removal narrows the space between CTCF and cohesin. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL20795
2 Samples

Download data: BW

Series

Accession:: GSE248736

ID:: 200248736

Select item 2002487314.

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry (ChIP-Seq)

(Submitter supplied) The transcription factor ZNF143 contains seven tandem zinc fingers and is involved in 3D genome construction; however, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes diverse genomic sites and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites and ZNF143 removal narrows the space between CTCF and cohesin. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL20795
1 Sample

Download data: BROADPEAK, BW

Series

Accession:: GSE248731

ID:: 200248731

PubMed Similar studies

Select item 2002366375.

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Homo sapiens

Type:: Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:: GPL24676 GPL20795
33 Samples

Download data: BEDGRAPH, BEDPE, BW, MCOOL, NARROWPEAK

Series

Accession:: GSE236637

ID:: 200236637

PubMed Similar studies

Select item 2002366366.

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [RNA-seq]

(Submitter supplied) The transcription factor ZNF143 contains seven tandem zinc fingers and is involved in 3D genome construction; however, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes diverse genomic sites and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites and ZNF143 removal narrows the space between CTCF and cohesin. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL20795
2 Samples

Download data: BW

Series

Accession:: GSE236636

ID:: 200236636

Select item 2002366357.

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [HiChIP]

(Submitter supplied) The transcription factor ZNF143 contains seven tandem zinc fingers and is involved in 3D genome construction; however, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes diverse genomic sites and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites and ZNF143 removal narrows the space between CTCF and cohesin. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:: GPL24676
7 Samples

Download data: BEDPE

Series

Accession:: GSE236635

ID:: 200236635

PubMed Similar studies

Select item 2002366348.

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [Hi-C]

(Submitter supplied) The transcription factor ZNF143 contains seven tandem zinc fingers and is involved in 3D genome construction; however, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes diverse genomic sites and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites and ZNF143 removal narrows the space between CTCF and cohesin. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL24676
6 Samples

Download data: MCOOL

Series

Accession:: GSE236634

ID:: 200236634

PubMed Similar studies

Select item 2002366339.

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [ChIP-seq]

(Submitter supplied) The transcription factor ZNF143 contains seven tandem zinc fingers and is involved in 3D genome construction; however, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes diverse genomic sites and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites and ZNF143 removal narrows the space between CTCF and cohesin. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL20795
2 Samples

Download data: BW, NARROWPEAK

Series

Accession:: GSE236633

ID:: 200236633

PubMed Similar studies

Select item 20023663210.

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [ChIP-nexus]

(Submitter supplied) The transcription factor ZNF143 contains seven tandem zinc fingers and is involved in 3D genome construction; however, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes diverse genomic sites and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites and ZNF143 removal narrows the space between CTCF and cohesin. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL20795
9 Samples

Download data: BW, NARROWPEAK

Series

Accession:: GSE236632

ID:: 200236632

PubMed Similar studies

Select item 20013112811.

CTCF and Cohesin link sex-biased distal regulatory elements to sex-biased gene expression in mouse liver

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:: GPL21103 GPL17021
43 Samples

Download data

Series

Accession:: GSE131128

ID:: 200131128

PubMed Full text in PMC Similar studies

Select item 20013091112.

4C-seq analysis of interactions with promoters and enhancers nearby five sex-specific genes, in male and female mouse liver

(Submitter supplied) Sequencing files provided here include 4C-seq experiments for a total of 6 viewpoints neighboring 5 highly sex-biased genes in mouse liver. These files are part of a larger study ("CTCF and Cohesin link sex-biased distal regulatory elements to sex-biased gene expression in mouse liver"), where we compare CTCF and cohesin binding in male and female mouse liver as well as differences in chromatin conformation (DNA looping).

Organism:: Mus musculus

Type:: Other

Platform:: GPL17021
36 Samples

Download data: BW

Series

Accession:: GSE130911

ID:: 200130911

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20013090813.

CTCF and Cohesin (Rad21) ChIP-seq in female mouse liver

(Submitter supplied) Sequencing files provided here include mouse liver ChIP-seq for CTCF and the cohesin subunit Rad21. These files are part of a larger study ("CTCF and Cohesin link sex-biased distal regulatory elements to sex-biased gene expression in mouse liver") where we compare CTCF and cohesin binding in male and female mouse liver as well as differences in chromatin conformation (DNA looping).

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21103
7 Samples

Download data: BED

Series

Accession:: GSE130908

ID:: 200130908

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20010299914.

Computational prediction of CTCF/cohesin-based intra-TAD (sbTAD) loops that insulate chromatin contacts and gene expression in mouse liver

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below, and presents the high throuput sequencing datasets that were generated as part of a larger study that investigates the role of CTCF and cohesin as key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. This study presents and validates a computational method to predict cohesin-and-CTCF binding sites that form intra-TAD DNA loops. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:: GPL21103 GPL17021 GPL13112
15 Samples

Download data

Series

Accession:: GSE102999

ID:: 200102999

PubMed Full text in PMC Similar studies

Select item 20010299715.

CTCF and Cohesin (Rad21) ChIP-seq in male mouse liver

(Submitter supplied) Sequencing files provided here include mouse liver ChIP-seq for CTCF and the cohesin subunit Rad21. These files are part of a larger study where we describe features of Topologically Associating Domains (TADs) and their impact on liver gene expression, then use these features to computationally predict subTAD structures not otherwise readily identifiable due to the low resolution of Hi-C. Our findings reveal that CTCF-based subTAD loops maintain key insulating properties of TADs, and support the proposal that subTADs are formed by the same loop extrusion mechanism and contribute to nuclear architecture as intra-TAD scaffolds that further constrain enhancer-promoter interactions. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL21103 GPL13112
7 Samples

Download data: BED

Series

Accession:: GSE102997

ID:: 200102997

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20010299816.

4C-seq analysis of interactions with the Albumin promoter in mouse liver

(Submitter supplied) Sequencing files provided here include mouse liver ChIP-seq for CTCF and the cohesin subunit Rad21, and 4C-seq analyses in male and female mouse liver centered at an Albumin promoter viewpoint. These files are part of a larger study where we describe features of Topologically Associating Domains (TADs) and their impact on liver gene expression, then use these features to computationally predict subTAD structures not otherwise readily identifiable due to the low resolution of Hi-C. more...

Organism:: Mus musculus

Type:: Other

Platform:: GPL17021
8 Samples

Download data: TXT

Series

Accession:: GSE102998

ID:: 200102998

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20013721617.

CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention [ChIP-seq & RNA-seq]

(Submitter supplied) The DNA-binding protein CTCF and the cohesin complex function together to shape chromatin architecture in mammalian cells, but the molecular details of this process remain unclear. We demonstrate that a 79 amino acid region within the CTCF N-terminal domain but not the C-terminus is necessary for cohesin positioning at CTCF binding sites and chromatin loop formation. However, the N-terminus of CTCF, when fused to artificial zinc fingers that do not bind to CTCF DNA binding sites was not sufficient to redirect cohesin to different genomic locations, indicating that cohesin positioning by CTCF does not involve direct protein-protein interactions with cohesin subunits. more...

Organism:: Homo sapiens; Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:: GPL13112 GPL11154
152 Samples

Download data: BEDGRAPH, TXT, XLSX

Series

Accession:: GSE137216

ID:: 200137216

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20013612218.

CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention

(Submitter supplied) The DNA-binding protein CTCF and the cohesin complex function together to shape chromatin architecture in mammalian cells, but the molecular details of this process remain unclear. We demonstrate that a 79 amino acid region within the CTCF N-terminal domain but not the C-terminus is necessary for cohesin positioning at CTCF binding sites and chromatin loop formation. However, the N-terminus of CTCF, when fused to artificial zinc fingers that do not bind to CTCF DNA binding sites was not sufficient to redirect cohesin to different genomic locations, indicating that cohesin positioning by CTCF does not involve direct protein-protein interactions with cohesin subunits. more...

Organism:: Mus musculus

Type:: Other

Platform:: GPL21103
5 Samples

Download data: HIC

Series

Accession:: GSE136122

ID:: 200136122

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20009099419.

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(Submitter supplied) The study investigates the nuclear organization and the binding dynamics of CTCF and cohesin by super-resolution microscopy and ChIP-seq. We determined the genome-wide binding profile of CTCF and Rad21 cohesin subunit in wild type mouse ES cells and compared them to a double FLAG-Halo-mCTCF/mRad21-SNAPf-V5 knock-in mES line, generated by CRISPR/Cas9-mediated genome editing to perform imaging experiments.

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21103
8 Samples

Download data: BW, TXT

Series

Accession:: GSE90994

ID:: 200090994

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20018748720.

Regulation of Chromatin Looping by CTCF and Cohesin

(Submitter supplied) As part of a study to understand the dynamics of chromatin looping and its regulation by CTCF and cohesin, we have determined the genome-wide binding profiles of CTCF and cohesin (Smc1a subunit) in a genome-edited mouse Embryonic Stem Cell (mESC) line referred to as clone C65. We have also performed 3D genome mapping using Micro-C in another genome-edited mESC line referred to as clone C36.

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:: GPL21103
9 Samples

Download data: BW, MCOOL

Series

Accession:: GSE187487

ID:: 200187487

PubMed Full text in PMC Similar studies SRA Run Selector

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