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

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Select item 2002662431.

PFKFB3 drives renal fibrosis through promoting histone lactylation-mediated NF- B activation [CUT&Tag]

(Submitter supplied) Persistently elevated glycolysis in kidney has been demonstrated to promote chronic kidney disease. However, the underlying mechanism remains largely unclear. Here, we observed that PFKFB3, a key glycolytic enzyme, was remarkably induced in kidney proximal tubular cells following ischemia-reperfusion injury in mice, as well as in multiple etiologies of chronic kidney disease patients. Proximal tubular epithelial-specific deletion of PFKFB3 significantly reduced renal lactate levels, mitigated inflammation and fibrosis, and preserved renal function in the IRI mouse model. more...

Organism:: Mus musculus

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

Platform:: GPL24247
6 Samples

Download data: BW

Series

Accession:: GSE266243

ID:: 200266243

Select item 2002660892.

Single-cell ATAC-seq analysis of mouse embryonic stem cells before and after Cohesin depletion

(Submitter supplied) The contrast between the disruption of genome topology upon cohesin loss and the lack of downstream gene expression changes instigates intense debates regarding the structure-function relationship between genome and gene regulation. Here, by analyzing transcriptome at the single-cell level, we discover that, instead of dictating population-wide gene expression levels, cohesin supplies a general function to neutralize stochastic co-expression tendency of cis-linked genes in single cells. more...

Organism:: Mus musculus

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

Platform:: GPL30172
4 Samples

Download data: BED, H5, MTX, TSV

Series

Accession:: GSE266089

ID:: 200266089

Select item 2002640303.

BRD9 regulates normal human hematopoietic stem cell function and lineage differentiation [ATAC-Seq]

(Submitter supplied) Bromodomain containing protein 9 (BRD9), a member of the non-canonical BRG1/BRM-associated factor (ncBAF) chromatin remodeling complex, has been implicated as a synthetic lethal target in AML but its function in normal human hematopoiesis is unknown. In hematopoietic stem and progenitor cells (HSPC) genomic or chemical inhibition of BRD9 led to a proliferative disadvantage and loss of stem cells in vitro. more...

Organism:: Homo sapiens

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

Platform:: GPL20301
9 Samples

Download data: BED, CSV

Series

Accession:: GSE264030

ID:: 200264030

Select item 2002634724.

Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions

(Submitter supplied) Visualizing and measuring molecular-scale interactions in living cells represents a major challenge, but recent advances in microscopy are bringing us closer to achieving this goal. Single-molecule super-resolution microscopy enables high-resolution and sensitive imaging of the positions and movement of molecules in living cells. HP1 proteins are important regulators of gene expression because they selectively bind and recognize H3K9 methylated (H3K9me) histones to form heterochromatin-associated protein complexes that silence gene expression. more...

Organism:: Schizosaccharomyces pombe

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

Platform:: GPL20584
5 Samples

Download data: BW

Series

Accession:: GSE263472

ID:: 200263472

Select item 2002630845.

Regulatory Functional Landscape of the HMX1 Gene for Normal Ear Development [CUT&RUN]

(Submitter supplied) Enhancers, through the combinatorial action of transcription factors (TFs), dictate both the spatial specificity and the levels of gene expression, and their aberrations can result in diseases. The association between HMX1 and its downstream enhancer with ear deformities has been previously documented. However, the pathogenic variations and molecular mechanisms underlying the bilateral constricted ear (BCE) malformations remain unclear. more...

Organism:: Homo sapiens

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

Platform:: GPL24676
6 Samples

Download data: BW

Series

Accession:: GSE263084

ID:: 200263084

Select item 2002561316.

Pharmaceutical inhibition of RAS overcomes cytokine mediated resistance to FLT3 inhibition in FLT3-ITD+ AML [ChIP-seq II]

(Submitter supplied) AML is characterised by a variety of co-occurring driver mutations in genes associated with cell signallingand growth regulationsuch as the FLT3-ITD. Inhibitors targeting FLT3 (FLT3i) are beingused to treat FLT3-ITD+ patients but most relapse.By profiling the gene regulatory networks of samples from patients before and after FLT3i treatment weobservedan increase in AP-1 mediated and a loss of RUNX1 mediated connections in treatment resistant cells. more...

Organism:: Homo sapiens

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

Platform:: GPL30173
4 Samples

Download data: BEDGRAPH

Series

Accession:: GSE256131

ID:: 200256131

Select item 2002549347.

ATAC-sequencing of Artemia cyst at 30min after embryonic diapause termination

(Submitter supplied) Embryonic diapause is a widely occurring evolutionary adaptation phenomenon in animals. Artemia is one of the classic animal models for diapause research. The current studies of Artemia diapause mainly focus on the induction and maintenance of the embryonic diapause, but there is little research on the molecular regulatory mechanism of Artemia embryonic diapause termination (EDT) and embryonic reactivation. more...

Organism:: Artemia parthenogenetic lineage

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

Platform:: GPL33946
3 Samples

Download data: XLSX

Series

Accession:: GSE254934

ID:: 200254934

Select item 2002547418.

Human cytomegalovirus extensively re-organizes the human genome, diminishing TEAD1 transcription factor activity

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

Organism:: Homo sapiens

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

Platform:: GPL24676
30 Samples

Download data: BW, NARROWPEAK, SF, TXT

Series

Accession:: GSE254741

ID:: 200254741

Select item 2002547369.

Human cytomegalovirus extensively re-organizes the human genome, diminishing TEAD1 transcription factor activity [ChIP-seq]

(Submitter supplied) Human cytomegalovirus (HCMV) infects up to 80% of the world’s population and is linked to serious morbidity in immunocompromised individuals and newborns. Here, using multiple genome-scale assays and computational approaches, we show that HCMV infection leads to widespread changes in chromatin accessibility and chromatin looping, with hundreds of thousands of human genomic regions affected 48 hours after infection. more...

Organism:: Homo sapiens

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

Platform:: GPL24676
12 Samples

Download data: BW, NARROWPEAK, TSV

Series

Accession:: GSE254736

ID:: 200254736

Select item 20025473410.

Human cytomegalovirus extensively re-organizes the human genome, diminishing TEAD1 transcription factor activity [ATAC-seq]

Organism:: Homo sapiens

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

Platform:: GPL24676
8 Samples

Download data: BW, NARROWPEAK, TSV

Series

Accession:: GSE254734

ID:: 200254734

Select item 20025372911.

Deep sequencing after alcelaphine gammaherpesvirus 1 infection reveals the nature of CD8+ T cell expansion and identify an essential viral protein for fatal bovine malignant catarrhal fever

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

Organism:: Bos taurus

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

Platforms:: GPL23055 GPL26012
31 Samples

Download data: BIGWIG, CSV, MTX, TSV, TXT

Series

Accession:: GSE253729

ID:: 200253729

Select item 20025372712.

Deep sequencing after alcelaphine gammaherpesvirus 1 infection reveals the nature of CD8+ T cell expansion and identify an essential viral protein for fatal bovine malignant catarrhal fever [ATAC-seq]

(Submitter supplied) Alcelaphine gammaherpesvirus 1 (AlHV-1) is a member of the Gammaherpesvirinae subfamily and establishes asymptomatic latent infection in its natural host species, the wildebeest. Cross-species transmission to various ruminant species including cattle can occur, resulting in the induction of malignant catarrhal fever (MCF), a deadly peripheral T cell lymphoproliferative disease. Here, we experimentally infected calves to confirm that AlHV-1 latency-associated gene expression is essential for persistent infection of CD8+ T cells and MCF development. more...

Organism:: Bos taurus

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

Platform:: GPL26012
13 Samples

Download data: BIGWIG

Series

Accession:: GSE253727

ID:: 200253727

Select item 20025216313.

Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors

(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 GPL24676 GPL18573
29 Samples

Download data: BW

Series

Accession:: GSE252163

ID:: 200252163

Select item 20025216014.

Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors [DNaseI-seq]

(Submitter supplied) Regulation of gene expression during cell development and differentiation is chiefly orchestrated by distal noncoding regulatory elements that precisely modulate cell selective gene activity. Gene therapy vectors rely on the cellular and context specificity of regulatory DNA elements to express therapeutic transgenes in the correct location and time. Here, we develop a straight-forward, one-shot approach to screen putative regulatory sequences identified in large-scale epigenomics profiling experiments for precise and programmable control of transgenes encoded within gene therapy viral vectors. more...

Organism:: Homo sapiens

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

Platforms:: GPL24676 GPL18573
3 Samples

Download data: BW

Series

Accession:: GSE252160

ID:: 200252160

Select item 20025215715.

Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors [CUT&RUN]

Organism:: Homo sapiens

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

Platform:: GPL18573
2 Samples

Download data: BW

Series

Accession:: GSE252157

ID:: 200252157

Select item 20024970316.

NAB2-STAT6 drives an EGR1-dependent neuroendocrine program in Solitary Fibrous Tumors

(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:: GPL30173
28 Samples

Download data: BW, TXT

Series

Accession:: GSE249703

ID:: 200249703

Select item 20024970117.

NAB2-STAT6 drives an EGR1-dependent neuroendocrine program in Solitary Fibrous Tumors (ChIP-Seq)

(Submitter supplied) The pathogenesis of many rare tumor types is poorly understood, preventing the design of effective treatments. Solitary Fibrous Tumors (SFTs) are neoplasms of mesenchymal origin that affect 1/1,000,000 individuals every year and are clinically assimilated to sarcomas. SFTs are commonly found throughout the body and can be surgically removed upon diagnosis. However, 30-40% of tumors become aggressive and can locally relapse or metastasize. more...