(genome binding/occupancy profiling by array[DataSet Type] OR genome b - GEO DataSets

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Select item 2002473511.

Mapping genotypes to chromatin accessibility profiles in single cells [scATAC-Seq; Pt08-19; Pt-02 DOGMAseq]

(Submitter supplied) Processed scATAC-seq sequencing data from myelofibrosis patients and raw sequencing data from scATAC-seq cell mixing experiments

Organism:: Homo sapiens

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

Platform:: GPL24676
15 Samples

Download data: CSV, MTX, TSV, TXT

Series

Accession:: GSE247351

ID:: 200247351

Select item 2002393242.

Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [Cut&Run]

(Submitter supplied) Human silencers have been shown to exist and regulate developmental gene expression. However, the functional importance of human silencers needs to be elucidated, such as whether they can form “super-silencers” and whether they are linked to cancer progression. Here, through interrogating two putative silencer components of FGF18 gene, we found that two nearby silencers can cooperate via compensatory chromatin interactions to form a “super-silencer”. more...

Organism:: Homo sapiens

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

Platform:: GPL24676
20 Samples

Download data: BW, NARROWPEAK

Series

Accession:: GSE239324

ID:: 200239324

Select item 2002393233.

Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [ATAC-seq]

Organism:: Homo sapiens

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

Platforms:: GPL24676 GPL20795
12 Samples

Download data: BW, NARROWPEAK

Series

Accession:: GSE239323

ID:: 200239323

Select item 2002049124.

Mapping genotypes to chromatin accessibility profiles in single cells

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

Organism:: Homo sapiens

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

Platform:: GPL24676
41 Samples

Download data: CSV, MTX, TSV, TXT

Series

Accession:: GSE204912

ID:: 200204912

Select item 2002032515.

Mapping genotypes to chromatin accessibility profiles in single cells [scATAC-seq; Pt01-07]

(Submitter supplied) Processed scATAC-seq sequencing data from myelofibrosis patients and raw sequencing data from scATAC-seq cell mixing experiments

Organism:: Homo sapiens

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

Platform:: GPL24676
13 Samples

Download data: TSV

Series

Accession:: GSE203251

ID:: 200203251

Select item 2001934896.

Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth

(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; Other

Platforms:: GPL20301 GPL20795 GPL24676
105 Samples

Download data: BED, HIC, TAB, TSV, TXT

Series

Accession:: GSE193489

ID:: 200193489

Select item 2001934847.

Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [HiChIP]

(Submitter supplied) Human silencers have been shown to exist and regulate developmental gene expression. However, the functional importance of human silencers need to be elucidated such as the working mode and whether they can form “super-silencers”. Here, through interrogating two putative silencer components of FGF18 gene, we found that two silencers can cooperate via compensated chromatin interactions to form the “super-silencer”. more...

Organism:: Homo sapiens

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

Platform:: GPL20301
1 Sample

Download data: BED, HIC

Series

Accession:: GSE193484

ID:: 200193484

SRA Run Selector

Select item 2001934818.

Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [ChIP-seq]

Organism:: Homo sapiens

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

Platform:: GPL20301
18 Samples

Download data: BROADPEAK, NARROWPEAK

Series

Accession:: GSE193481

ID:: 200193481

SRA Run Selector

Select item 2001885599.

Shared patterns of glial transcriptional dysregulation link Huntington's disease and schizophrenia

(Submitter supplied) Huntington’s disease (HD) and juvenile-onset schizophrenia (SCZ) have long been regarded as distinct disorders. However, both manifest cell-intrinsic abnormalities in glial differentiation, with resultant astrocytic dysfunction and hypomyelination. To assess whether a common mechanism might underlie the similar glial pathology of these otherwise disparate conditions, we utilized comparative correlation network approaches to analyze RNA-seq data from human glial progenitor cells (hGPCs) produced from disease-derived pluripotent stem cells. more...

Organism:: Rattus norvegicus; Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platform:: GPL18573
2 Samples

Download data: BW, NARROWPEAK, TXT

Series

Accession:: GSE188559

ID:: 200188559

SRA Run Selector

Select item 20016610310.

HMGN5, an RNA and Nucleosome binding protein required for chromatin de-condensation and gene activation

(Submitter supplied) The packaging of DNA into chromatin and its compaction within cells renders the underlying DNA template un-accessible for processes like transcription, replication and repair. Active mechanisms as chromatin modifying activities or the association with non-coding RNAs can de-condense chromatin, rendering it accessible for the DNA dependent processes. High mobility group proteins (HMG) are small architectural chromatin proteins that were shown to contribute to the regulation of chromatin accessibility and condensation. more...

Organism:: Homo sapiens

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

Platforms:: GPL11154 GPL15433
13 Samples

Download data

Series

Accession:: GSE166103

ID:: 200166103

Select item 20016609811.

HMGN5, an RNA and Nucleosome binding protein required for chromatin de-condensation and gene activation [ChIP-seq]

(Submitter supplied) HMGN5 is a member of the HMGN family that de-compacts chromatin and regulates gene expression. Chromatin-associated RNAs are known to play a major role in controlling gene expression and chromatin architecture. We recently showed that RNA is required to open chromatin structure in Drosophila. A potential involvement of RNA in the HMGN5-dependent opening of chromatin has not been studied so far. Here we revealed that HMGN5 has a novel and specific RNA binding activity, which is extended to the HMGN family. more...

Organism:: Homo sapiens

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

Platform:: GPL15433
5 Samples

Download data: TXT

Series

Accession:: GSE166098

ID:: 200166098

SRA Run Selector

Select item 20026669112.

KAP1 negatively regulates elongation kinetics to activate signal-induced transcription [ChIP-Seq]

(Submitter supplied) Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction are still unfolding. By combining an acute depletion system with high resolution genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. more...

Organism:: Homo sapiens

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

Platform:: GPL30173
51 Samples

Download data

Series

Accession:: GSE266691

ID:: 200266691

Select item 20026649013.

ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes (ATAC-seq)

(Submitter supplied) Transcription factors bind to sequence motifs and act as activators or repressors. Transcription factors interface with a constellation of accessory cofactors to regulate distinct mechanistic steps to regulate transcription. We rapidly degraded the essential and ubiquitously expressed transcription factor ZNF143 to determine its function in the transcription cycle. ZNF143 facilitates RNA Polymerase initiation and activates gene expression. more...

Organism:: Homo sapiens

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

Platform:: GPL21697
16 Samples

Download data: BED, BIGWIG

Series

Accession:: GSE266490

ID:: 200266490

Select item 20026648914.

ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes (ChIP-seq)

Organism:: Homo sapiens

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

Platform:: GPL21697
16 Samples

Download data: BED, BIGWIG

Series

Accession:: GSE266489

ID:: 200266489

Select item 20026628815.

NR4A1 transcriptionally regulates the differentiation of stem-like CD8+ T cells in the tumor microenvironment

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

Organism:: Mus musculus

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

Platforms:: GPL23479 GPL30215
20 Samples

Download data: BW

Series

Accession:: GSE266288

ID:: 200266288

Select item 20026331716.

Nuclear receptor Nur77 and Yin-Yang 1 synergistically increase mitochondrial abundance and activity in macrophages.

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

Organism:: Mus musculus

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

Platform:: GPL17021
9 Samples

Download data: BED, TXT

Series

Accession:: GSE263317

ID:: 200263317

Select item 20026331517.

Nuclear receptor Nur77 and Yin-Yang 1 synergistically increase mitochondrial abundance and activity in macrophages [ChIP-seq]

(Submitter supplied) Mitochondrial biogenesis requires precise regulation of both mitochondrial-encoded and nuclear-encoded genes. Nuclear receptor Nur77 is known to regulate mitochondrial metabolism in macrophages and skeletal muscle cells. Here, we compared genome-wide Nur77 binding site and target gene expression in these two cell types, which revealed conserved roles for this nuclear receptor in the regulation of nuclear-encoded mitochondrial ribosomal proteins (MRP) and enrichment of motifs for the transcription factor Yin-Yang 1 (YY1). more...

Organism:: Mus musculus

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

Platform:: GPL17021
3 Samples

Download data: BED

Series

Accession:: GSE263315

ID:: 200263315

Select item 20025339118.

Genomic context-dependent histone H3K36 methylation by Drosophila methyltransferases

(Submitter supplied) How different histone methyltransferases (HMT) cooperate to progressively catalyze different methylation states of the same residue as well the functional consequences of the different methylation states are not well known. Here, we address in the context of Drosophila H3K36 methylation by using single and combinatorial RNAi of HMTs along with genome-wide MNase-ChIPseq analyses. Our study reveals that K36me1/2/3 each mark distinct chromatin compartments. more...

Organism:: Drosophila melanogaster

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

Platforms:: GPL33093 GPL19951
107 Samples

Download data: BED, BW, TXT

Series

Accession:: GSE253391

ID:: 200253391

Select item 20024804819.

Vaccinia virus infection induces concurrent alterations in host chromatin architecture, accessibility, and gene expression [ATAC-seq]

(Submitter supplied) Genomic DNA folds into complex configurations that produce particular local and globalstructures thought to profoundly impact genome function. To understand the dynamic nature ofthis relationship, we investigated the extent of host chromatin structural and functional changesin response to a viral agent. We performed comprehensive assessments of host architecture (Hi-C), accessibility (ATAC-seq), and gene expression (RNA-seq) in a paired manner in response toattenuated vaccinia (smallpox) virus. more...

Organism:: Chlorocebus sabaeus

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

Platform:: GPL30937
12 Samples

Download data: BW

Series

Accession:: GSE248048

ID:: 200248048

Select item 20024621820.

KAP1 regulates elongation kinetics to activate signal-induced transcription

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

Organism:: Homo sapiens

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

Platform:: GPL30173
79 Samples

Download data

Series

Accession:: GSE246218

ID:: 200246218

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