Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

WDR26 depletion alters chromatin accessibility and gene expression profiles in mammalian cells [ATAC-seq]

ABSTRACT: WDR26 depletion alters chromatin accessibility and gene expression profiles in mammalian cells [ATAC-seq]

PROVIDER: PRJNA1139849 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR29974505_1.fastq.gz	Fastqsanger.gz
	SRR29974505_2.fastq.gz	Fastqsanger.gz
	SRR29974506_1.fastq.gz	Fastqsanger.gz
	SRR29974506_2.fastq.gz	Fastqsanger.gz
	SRR29974507_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

WDR26 depletion alters chromatin accessibility and gene expression profiles in mammalian cells [RNA-seq]

Project description:WDR26 depletion alters chromatin accessibility and gene expression profiles in mammalian cells [RNA-seq]

| PRJNA1139852 | ENA

WDR26 depletion alters chromatin accessibility and gene expression profiles in mammalian cells [ATAC-seq]

Project description:WD-repeat containing protein 26 (WDR26) is an essential component of the CTLH E3 ligase complex. Mutations in WDR26 lead to Skraban-Deardorff, an intellectual disability syndrome with clinical features resembling other disorders arising from defects in transcriptional regulation and chromatin structure. However, the role of WDR26 and its associated CTLH complex in regulating chromatin or transcription has not been elucidated. Here, we assessed how loss of WDR26 affects chromatin accessibility and gene expression. Transcriptome analysis of WDR26-null HeLa cells revealed over 2000 differentially expressed genes, while ATAC-Seq analysis showed over 32 000 differentially accessible chromatin regions, the majority mapping to intergenic and intronic regions and 13% mapping to promoters. Above all, we found that WDR26 loss affected expression of genes regulated by AP-1 and NF-1 transcription factors and resulted in dramatic changes in their chromatin accessibility. Overall, our analyses implicate WDR26 and the CTLH complex in chromatin regulation.

2025-01-21 | GSE273059 | GEO

WDR26 depletion alters chromatin accessibility and gene expression profiles in mammalian cells [RNA-seq]

2025-01-21 | GSE273060 | GEO

Phosphate depletion in mammalian cells

Project description:Phosphate depletion in mammalian cells

| PRJNA867397 | ENA

CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters

Project description:This SuperSeries is composed of the following subset Series: GSE38560: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (RNA-seq) GSE38561: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (ChIP-seq) GSE38562: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (genomic SEQ) GSE38563: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (MNase-seq) GSE38564: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (5) Refer to individual Series

2012-06-11 | E-GEOD-38577 | biostudies-arrayexpress

Acute depletion of CTCF rewires genome-wide chromatin accessibility

Project description:The transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studies. However, acute depletion of CTCF globally reduces chromatin interactions but does not significantly alter transcription. Here we systematically integrated multi-omics data including ATAC-seq, RNA-seq, WGBS, Hi-C, Cut&Run, CRISPR-Cas9 survival dropout screening, time-solved deep proteomic and phosphoproteomic analyses in cells carrying auxin-induced degron at endogenous CTCF locus. Acute CTCF protein degradation markedly rewired genome-wide chromatin accessibility. Increased accessible chromatin regions were largely located adjacent to CTCF-binding sites at promoter regions and insulator sites and were associated with enhanced transcription of nearby genes. In addition, we used CTCF-associated multi-omics data to establish a combinatorial data analysis pipeline to discover CTCF co-regulatory partners in regulating downstream gene expression. We successfully identified 40 candidates, including multiple established partners (i.e., MYC) supported by all layers of evidence. Interestingly, many CTCF co-regulators (e.g., YY1, ZBTB7A) that have evident alterations of respective downstream gene expression do not show changes at their expression levels across the multi-omics measurements upon acute CTCF loss, highlighting the strength of our system to discover hidden co-regulatory partners associated with CTCF-mediated transcription. This study highlights CTCF loss rewires genome-wide chromatin accessibility, which plays a critical role in transcriptional regulation

2021-07-04 | PXD026484 | Pride

Confined Migration Induces Heterochromatin Formation and Alters Chromatin Accessibility

Project description:Confined Migration Induces Heterochromatin Formation and Alters Chromatin Accessibility

| PRJNA751211 | ENA

Mammalian SWI/SNF continuously restores local accessibility to chromatin

Project description:Mammalian SWI/SNF continuously restores local accessibility to chromatin

| PRJNA664941 | ENA

Acute depletion of CTCF rewires genome-wide chromatin accessibility

Project description:Acute depletion of CTCF rewires genome-wide chromatin accessibility

| PRJNA641828 | ENA

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

Project description:A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility