Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Hi-C in wild-type and SmcHD1 MommeD1 MEFs, first set

ABSTRACT: Hi-C in wild-type and SmcHD1 MommeD1 MEFs, first set

PROVIDER: PRJNA476700 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7362900_1.fastq.gz	Fastqsanger.gz
	SRR7362900_2.fastq.gz	Fastqsanger.gz
	SRR7362901_1.fastq.gz	Fastqsanger.gz
	SRR7362901_2.fastq.gz	Fastqsanger.gz
	SRR7362902_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Hi-C in wild-type, SmcHD1 MommeD1mut and somKO MEFs

Project description:Hi-C in wild-type, SmcHD1 MommeD1mut and somKO MEFs

| PRJNA495638 | ENA

The effect on gene expression of Smchd1 deletion in primary MEFs, transformed MEFs and MEF tumours

Project description:Smchd1 appears to act as a tumour suppressor in the transformed fibroblast model. We find gene expression differences are most pronounced in the transformed MEFs. We always detect a small number of clustered genes and imprinted genes as differentially expressed, along with others involved in tumorigenesis. The microarrays compared Smchd1 null and Smchd1 wildtype samples from different cell types (primary MEFs, transformed MEFs, tumours derived from transformed MEFs). Wildtype mice are FVB/N and Smchd1 null mice have the MommeD1 point mutation on a FBV/N background.

2012-09-30 | E-GEOD-40734 | biostudies-arrayexpress

In situ Hi-C in Smchd1 wild-type and Smchd1 deleted neural stem 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 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 | GSE111720 | GEO

Hi-C in wild-type and SmcHD1 MommeD1 MEFs, first set

Project description:In this study we investigate the role of the non-canonical SMC family protein, SmcHD1in the X inactivation.

2018-11-07 | GSE115983 | GEO

In situ Hi-C in Smchd1 wild-type and Smchd1 deleted neural stem cells. [II]

2018-06-30 | GSE115933 | GEO

The effect on gene expression of Smchd1 deletion in primary MEFs, transformed MEFs and MEF tumours

2012-09-30 | GSE40734 | GEO

The effect on gene expression of Smchd1 deletion in various cell types

Project description:This SuperSeries is composed of the following subset Series: GSE40734: The effect on gene expression of Smchd1 deletion in primary MEFs, transformed MEFs and MEF tumours GSE40879: The effect on gene expression of Smchd1 deletion in pre-B cells from E17.5 Eµ-Myc embryos GSE40880: The effect on gene expression of Smchd1 deletion in end stage lymphomas GSE40881: The effect on gene expression of Smchd1 deletion in premalignant pre-B cells Refer to the individual subSeries. NOTE: all the cell types need to be analyzed separately.

2012-09-30 | E-GEOD-40992 | biostudies-arrayexpress

chrRNA-seq in wild-type, SmcHD1 MommeD1mut and somKO MEFs

Project description:chrRNA-seq in wild-type, SmcHD1 MommeD1mut and somKO MEFs

| PRJNA496037 | ENA

In situ Hi-C in Smchd1 wild-type and Smchd1 deleted neural stem cells.

Project description:In situ Hi-C in Smchd1 wild-type and Smchd1 deleted neural stem cells.

| PRJNA437969 | ENA

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

2018-06-30 | GSE111721 | GEO