ChIP-Seq analysis of SMARCA4 binding sites in human NSC
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA515001 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8439460.fastq.gz | Fastqsanger.gz | |||
| SRR8439461.fastq.gz | Fastqsanger.gz | |||
| SRR8439462.fastq.gz | Fastqsanger.gz | |||
| SRR8439463.fastq.gz | Fastqsanger.gz | |||
| SRR8439464.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 14 |
Similar Datasets
Project description:We performed large-scale, pooled shRNA screens targeting 538 epigenetic regulators in genetically identical human stem cells, where each gene was targeted on avarage by 12 shRNAs. CD34+ HSPCs, used as a starting point of the study, were reprogrammed to iPSCs, which were differentiated to NSC. These cells were transduced with the pooled shRNA library and samples were collected 2 days post transduction (dpt), 12 dpt, and 22dpt - allowing 5 cell doublings. PCR amplified gDNA carrying the shRNA barcodes was sequenced on a HiSeq2500 Illumina sequencer. Analysis of NGS results, based on the change of shRNA representation (read count) and represented by z-scores, identified SMARCA4 as a differential regulator (SMARCA4 shRNAs were depleted in HSPC vs enriched in NSC sreens). We performed RNA-seq experiments as part of the characterization dataset for the isogenic HSPC, HSPC-derived iPSC, and iPSC-derived NSC. RNA samples from CD34+ HSPC were harvested in parallel to gDNA isolation on 12- and 22-days post transduction, during the RNAi screen. In addition, untreated iPSC and NSC RNA samples were sequenced as part of their characterization. RNA samples were sequenced with poly-dT enrichment using single-end sequencing. Each sample was sequenced at a depth of yielding at least 20 million reads. We performed a ChIP-seq analysis of the SMARCA4 binding sites in hNSC, which we identified in the large-scale RNAi screens as a candidate, involved in regulation of self-renewal and differentiation. The pull-down experiment was performed on the untreated NSCs. We show that SMARCA4 has a prominent binding tendency for the TSS throughout the genome, suggesting a role for SMARCA4 in transcriptional regulation.
2019-04-09 | GSE125033 | GEO
Project description:SMARCA4 Rescue Profiling [ChIP]
| PRJNA547548 | ENA
Project description:Mutations in SMARCA4, a central ATPase of the human BAF/PBAF chromatin remodeling complexes, cause developmental abnormalities and promote cancer development. The pathogenic effects of SMARCA4 loss are often linked to the de-regulation of a relatively small number of key target genes. Here, to understand how chromatin remodeling by SMARCA4 results in specific transcriptional perturbations, we used genome engineering to correct a homozygous mutation in SMARCA4 in the well-characterized lung adenocarcinoma A549 cell line and profiled changes in SMARCA2/4 occupancy, chromatin accessibility, histone marks and transcription. Restoration of SMARCA4 causes a dramatic increase in chromatin accessibility at low affinity TF binding sites. Despite the widespread increase in chromatin accessibility, we observe comparatively attenuated changes in gene expression. Although there is a marked correlation between the number of local activated DHSs and the transcriptional responsivity of a gene, the influence of distal DHSs appears modified by a gene's promoter architecture and domain-scale chromatin organization. The largest changes in expression occur for genes in isolated, SMARCA4 sensitive chromatin domains that undergo region-wide chromatin remodeling upon reintroduction of SMARCA4. Our results reveal that interactions between distal enhancers, genome organization, and promoter architecture add transcriptional specificity to the global chromatin effects of BAF/PBAF complex perturbation and target the response to key developmental pathways.
2020-05-20 | GSE132290 | GEO
Project description:ChIP-Seq of Yy1 binding sites in melanoma cells.
| PRJEB21646 | ENA
Project description:ChIP-Seq of PRDM16 binding sites in E14 MGE
| PRJNA670345 | ENA
Project description:The packaging of DNA into chromatin plays an important role in transcriptional regulation and nuclear processes. Brahma related gene-1 SMARCA4 (also known as BRG1), the essential ATPase subunit of the mammalian SWI/SNF chromatin remodeling complex, uses the energy from ATP hydrolysis to disrupt nucleosomes at target regions. Although the transcriptional role of SMARCA4 at gene promoters is well-studied, less is known about its role in higher-order genome organization. SMARCA4 knockdown in human mammary epithelial MCF-10A cells resulted in 176 up-regulated genes, including many related to lipid and calcium metabolism, and 1292 down-regulated genes, some of which encode extracellular matrix (ECM) components that can exert mechanical forces and affect nuclear structure. ChIP-seq analysis of SMARCA4 localization and SMARCA4-bound super-enhancers demonstrated extensive binding at intergenic regions. Furthermore, Hi-C analysis showed extensive SMARCA4-mediated alterations in higher-order genome organization at multiple resolutions. First, SMARCA4 knockdown resulted in clustering of intra- and inter- sub-telomeric regions, demonstrating a novel role for SMARCA4 in telomere organization. SMARCA4 binding was enriched at TAD (Topologically Associating Domain) boundaries, and SMARCA4 knockdown resulted in weakening of TAD boundary strength. Taken together, these findings provide a dynamic view of SMARCA4-dependent changes in higher-order chromatin organization and gene expression, identifying SMARCA4 as a novel component of chromatin organization. Hi-C and RNA-seq experiments were conducted in MCF-10A shSCRAM and shSMARCA4 cells. SMARCA4 ChIP-seq was conducted in wildtype MCF-10A cells.
2016-06-02 | E-GEOD-74716 | biostudies-arrayexpress
Project description:To reveal the genome-wide targets of SWI/SNF complexes in neuroblastoma cells, we performed ChIP-seq of SMARCA4 (BRG1) in IMR-32, KELLY, and SK-N-DZ cells. We used these libraries to examine chromatin occupancy profiling. Analysis of locations reveal that SMARCA4 targets directly regulate sites regulated by the neuroblastoma core regulatory circuitry.
2023-10-24 | GSE190707 | GEO
Project description:To reveal the genome-wide targets of SWI/SNF complexes in neuroblastoma cells, we performed ATAC-seq in IMR-32 cells with or without SMARCA4 inactivation. To identify changes in DNA accessibility following SMARCA4 inactivation, we used either the small-molecule catalytic inhibitor BRM014, auxin-induced degradation of IMR-32 cells engineered with SMARCA4 tagged to the minimal auxin-induced degron (SMARCA4-mAID), or the corresponding vehicle controls. Analysis of these locations reveal that SMARCA4-dependent sites are located at enhancers used by the neuroblastoma core regulatory circuitry.
2023-10-24 | GSE190706 | GEO
Project description:Using ChIP-seq, we identified the genome-wide occupancy of SMARCA2 and SMARCA4 in lung cancer cells (NCI-H1944) reconstituted with SMARCA4 WT. We also determined how SMARCA4 occupancy changed in NCI-H1944 after SMARCA2 depletion.
2020-09-10 | GSE147201 | GEO
Project description:ChIP-Seq analysis of PPARγ binding sites in iNKT cells
| PRJNA545303 | ENA