Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Allele-specific H3K27me3, H3K27ac and Ctcf ChIP-seq in Smchd1 control and Smchd1 deleted female neural stem cells. [H3K27ac]

ABSTRACT: Allele-specific H3K27me3, H3K27ac and Ctcf ChIP-seq in Smchd1 control and Smchd1 deleted female neural stem cells. [H3K27ac]

PROVIDER: PRJNA439003 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6862660_1.fastq.gz	Fastqsanger.gz
	SRR6862660_2.fastq.gz	Fastqsanger.gz
	SRR6862657_1.fastq.gz	Fastqsanger.gz
	SRR6862657_2.fastq.gz	Fastqsanger.gz
	SRR6862658_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Allele-specific H3K27me3, H3K27ac and Ctcf ChIP-seq in Smchd1 control and Smchd1 deleted female neural stem cells. [H3K27me3]

Project description:Allele-specific H3K27me3, H3K27ac and Ctcf ChIP-seq in Smchd1 control and Smchd1 deleted female neural stem cells. [H3K27me3]

| PRJNA439001 | ENA

Allele-specific H3K27me3, H3K27ac and Ctcf ChIP-seq in Smchd1 control and Smchd1 deleted female neural stem cells. [H3K27ac]

Project description:We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. We additionally analysed Smchd1 binding genome-wide using ChIP-seq. Together, we find that deletion of Smchd1 alters chromosome conformation at Smchd1 target genes including the inactive X chromosome, Hox genes and imprinted loc. Smchd1 deletion results in gain in Ctcf binding and activation of enhancers. We propose Smchd1 functions by limiting Ctcf-mediated chromosome looping.

2018-06-30 | GSE112046 | GEO

Allele-specific H3K27me3, H3K27ac and Ctcf ChIP-seq in Smchd1 control and Smchd1 deleted female neural stem cells. [H3K27me3]

2018-06-30 | GSE112045 | GEO

Allele-specific RNA-seq in Smchd1 control and Smchd1 deleted female neural stem cells.

2018-06-30 | GSE112043 | GEO

Allele-specific RNA-seq in Smchd1 control and Smchd1 deleted female neural stem cells.

Project description:Allele-specific RNA-seq in Smchd1 control and Smchd1 deleted female neural stem cells.

| PRJNA439002 | ENA

ATAC-seq in Smchd1 wild-type and Smchd1 deleted neural stem cells.

2018-06-30 | GSE111721 | GEO

RRBS in Smchd1 control and Smchd1 deleted male and female neural stem cells.

2018-06-30 | GSE115932 | GEO

RNA-seq in Smchd1 wild-type and Smchd1 deleted differentiating male ES cells.

Project description:We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. We additionally analysed Smchd1 binding genome-wide using ChIP-seq. Together, we find that deletion of Smchd1 alters chromosome conformation at Smchd1 target genes including the inactive X chromosome, Hox genes and imprinted loci. Smchd1 deletion in differentiating ES cells results in failed Hox gene silencing. Smchd1 deletion results in gain in Ctcf binding and activation of enhancers. We propose Smchd1 functions by limiting Ctcf-mediated chromosome looping.

2018-06-30 | GSE111724 | GEO

RNA-seq in Smchd1 control and Smchd1 deleted male and female neural stem cells.

2018-06-30 | GSE111723 | GEO