Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

WGBS of WT and Smchd1-KO ES cells

ABSTRACT: WGBS of WT and Smchd1-KO ES cells

PROVIDER: PRJNA521987 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR8568290_1.fastq.gz	Fastqsanger.gz
	SRR8568290_2.fastq.gz	Fastqsanger.gz
	SRR8568291_1.fastq.gz	Fastqsanger.gz
	SRR8568291_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 23

Similar Datasets

WGBS of WT and Smchd1-KO ES cells

Project description:We performed the whole genome bisulfite sequencing to detect the DNA methylation between the wild type ES cells and Smchd1 mutant ES cells

2021-01-27 | GSE126466 | GEO

RNAseq of Wildtype, Smchd1 KO, Dux KO, Double KO, Tet-TKO and quadurple KO ES cells

Project description:RNAseq was performed by to compare gene expression between wildtype and Smchd1 KO ES cells, the gene expression pattern in Dux KO mutants , Double KO mutant Tet-TKO mutants and Tet TKO plus SMCKHD1 KO mutants were analyzed by RNAseq.

2021-01-27 | GSE126467 | GEO

RNAseq of Wildtype, Smchd1 KO, Dux KO, Double KO, Tet-TKO and quadurple KO ES cells

Project description:RNAseq of Wildtype, Smchd1 KO, Dux KO, Double KO, Tet-TKO and quadurple KO ES cells

| PRJNA521986 | ENA

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 and expression profile of WT and ZFP57 KO ES cells

Project description:RNA-seq and expression profile of WT and ZFP57 KO ES cells

2011-11-07 | GSE31182 | GEO

Investigating the role of SMCHD1 in de novo X chromosome inactivation

Project description:To investigate the effect of Smchd1 ablation on de novo X chromosome inactivation (XCI), we derived clonal neural progenitor cells (NPCs) from Smchd1+/+ (wild-type, WT) and Smchd1-/- mouse embryonic stem cells (ES cells; ESC). We generated allele-specific RNA-seq datasets from WT and Smchd1-/- NPCs to examine the effect of Smchd1 ablation on gene silencing. In addition, we produced allele-specific ChIP-seq profiles of H3K4me3, H3K27me3, CTCF, and RAD21 and Xist CHART-seq profiles in WT and Smchd1-/- NPCs to investigate the role of SMCHD1 on the distribution of euchromatin, facultative heterochromatin, architectural proteins, and Xist RNA on the inactive X chromosome (Xi). To determine the localization of SMCHD1 on the Xi, we employed allele-specific DamID-seq to map SMCHD1-binding regions in female mouse embryonic fibroblasts. Furthermore, we performed in situ Hi-C on WT NPCs, Smchd1-/- NPCs, and female ES cells undergoing XCI, in order to explore the role of SMCHD1 in regulating the higher-order structure of the Xi.

2018-06-07 | GSE99991 | GEO

Transcriptome analysis of WT and ATRX KO Cast x 129 mouse ES cells

Project description:Analysis of gene expression in WT and ATRX KO Cast x 129 Mouse ES cells

2015-04-16 | GSE59269 | GEO

RNAseq data from ES and differentiated cells in Chd8 WT vs Chd8 KD and Chd8 KO cells

Project description:In this study, we compare the transcriptomic difference between WT and Chd8 depleted ES aand differentiating ES cells. We report significant differences between Chd8 WT and KD/KO cell lines.

2021-04-27 | GSE166858 | GEO

Genome-wide ChIP seq of H3.3 in WT and ATRX KO mouse ES cells

Project description:Regions of H3.3 binding in WT and ATRX KO mouse ES cells were identified by ChIP seq

2015-04-16 | GSE59270 | GEO

Genome-wide ChIP seq of H3.3 in WT and ATRX KO mouse ES cells

Project description:Regions of H3.3 binding in WT and ATRX KO mouse ES cells were identified by ChIP seq Chip-seq experiements were performed in WT and ATRX KO E14 mouse ES cells

2015-04-16 | E-GEOD-59270 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data