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BRG1 occupancy profiling by high throughput sequencing from control and PTEN knockdown 22RV-1 cells

ABSTRACT: BRG1 occupancy profiling by high throughput sequencing from control and PTEN knockdown 22RV-1 cells

PROVIDER: PRJNA475577 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7290305.fastq.gz	Fastqsanger.gz
	SRR7290306.fastq.gz	Fastqsanger.gz
	SRR7290307.fastq.gz	Fastqsanger.gz

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BRG1 occupancy profiling by high throughput sequencing from control and PTEN knockdown 22RV-1 cells

Project description:To identify the downstream targets and pathways mediated by BRG1, chromatin immunoprecipitation followed by sequencing (ChIP–seq) was performed in control and PTEN-knockdown 22RV-1 cells. Total 6279 genes showed the enhanced BRG1 occupancies in PTEN-knockdown cells as compared to that in control cells. Genome-wide analysis revealed that PTEN loss lead to increase BRG1 intervals specifically localized at enhancers, but not distal promoter regions. We therefore reasoned ablation of BRG1 might impair enhancer configurations in PTEN-deficient cells.

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Transcriptome analysis of control and BRG1-depleted 22RV-1 cells with or without PTEN ablation

Project description:We conduct transcriptome comparison of control and BRG1-depleted 22RV-1 cells with or without PTEN ablation to gain genomic insights on the biological processes that BRG1 is involved in depend on PTEN deletion. Through unsupervised cluster analysis of differentially expressed genes (DEGs), we found the expressions of 5489 genes were significantly altered in PTEN/BRG1 double knockdown cells, whereas they remained consistent or opposite pattern in control, BRG1-KD and PTEN-KD cells. Differential principal component analysis (PCA) suggested ablation of BRG1 in PTEN-depleted cells forced the cells undergoing a distinct transcriptome as compared to the others. In keeping with these findings, KEGG-DEGs relationship network indicated BRG1 loss in PTEN-deficient cells significantly altered the process related to “Prostate cancer”, “Cell cycle”, “Cell motility” and etc.

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Compare chromatin open regions (OCRs) between PTEN-KD and PTEN/BRG1-KD 22RV-1 cells by ATAC-Seq

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Genome-wide occupancy of chromatin remodeller SMARCAL1 and BRG1 in human cells

Project description:In this study we report genome wide occupancy of SMARCAL1 and BRG1 in control HeLa cells. Our analysis showed binding of these two remodellers on DNA damage response gene, chromatin remodellers, cell cycle and apoptosis regulating genes.

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2023-02-15 | PXD029647 | Pride

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