Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ATAC-Seq of Diversity Outbred mouse embryonic stem cells

ABSTRACT: ATAC-Seq of Diversity Outbred mouse embryonic stem cells

PROVIDER: PRJEB36566 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3866810.fastq.gz	Fastqsanger.gz
	ERR3866820.fastq.gz	Fastqsanger.gz
	ERR3866830.fastq.gz	Fastqsanger.gz
	ERR3866840.fastq.gz	Fastqsanger.gz
	ERR3866850.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 1152

Similar Datasets

ATAC-Seq of Diversity Outbred mouse embryonic stem cells

Project description:We measured genome-wide chromatin accessibility of embryonic stem cells derived from Diversity Outbred mice. We cultured cells in media with LIF + GSK3-beta inhibitor CHIR99021.

2020-08-13 | E-MTAB-8759 | biostudies-arrayexpress

RNA-Seq of Diversity Outbred mouse embryonic stem cells

Project description:We measured genome-wide gene expression of embryonic stem cells derived from Diversity Outbred mice. We cultured cells in media with LIF + GSK3-beta inhibitor CHIR99021. All lines were passage 3-8 when RNA was collected. We obtained RNA-Seq from technical replicate cultures for three cell lines.

2020-08-13 | E-MTAB-7728 | biostudies-arrayexpress

RNA-Seq of Diversity Outbred mouse embryonic stem cells

Project description:RNA-Seq of Diversity Outbred mouse embryonic stem cells

| PRJEB31538 | ENA

Mus musculus strain:Diversity Outbred

Project description:Diversity Outbred Liver RNASeq

| PRJNA356251 | ENA

Project description:SAGA and ATAC are two related transcriptional coactivator complexes, sharing the same histone acetyltransferase (HAT) subunit. The HAT activities of SAGA and ATAC are required for metazoan development but the precise role of the two complexes in RNA polymerase II transcription in mammals is less understood. To determine whether SAGA and ATAC have redundant or specific functions dependent on their HAT activities, we compared the effects of HAT inactivation in each complex with that of inactivation of either SAGA or ATAC core subunits in mouse embryonic stem cells (ESCs). We show that core subunits of SAGA or ATAC subunits are required for complex assembly, mouse ESC growth and self-renewal. Additionally, ATAC, but not SAGA subunits are required for ESC viability by regulating the transcription of translation-related genes. Surprisingly, depletion of specific or shared HAT module subunits caused a global decrease in histone H3K9 acetylation, but did not result in significant phenotypic or transcriptional defects. Thus, our results indicate that SAGA and ATAC are differentially required for viability and self-renewal of mouse ESCs by regulating transcription through different pathways, in a HAT-independent manner.

2021-08-11 | PXD027026 | Pride

Metabolomics Workbench ST000003 - GNPS - Metabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells

Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis

2018-08-02 | MSV000082680 | GNPS

RNA-Seq of hippocampus in Diversity Outbred mice

Project description:To understand the genetic regulation of gene expression and patterns of gene co-expression, we sequenced the transcriptome of the hippocampus of 258 Diversity Outbred (DO) mice of both sexes. DO mice (fourth and fifth generations of outcrossing) were sacrificed between 6-8 weeks of age and hippocampus dissected. Total hippocampal RNA was isolated using a TRIzol Plus RNA purification kit (Life Technologies) and mRNA sequencing library was prepared using a TruSeq kit (Illumina), both according to manufacturer's protocols. Paired-end 100bp reads were obtained using the Illumina HiSeq 2000.

2019-05-01 | E-MTAB-7637 | biostudies-arrayexpress

ATAC-seq of mouse embryonic stem cells

Project description:To identify the accessible chromatin in wild-type mouse embryonic stem cells (mESCs), we performed ATAC-seq in mESCs.

2021-01-05 | E-MTAB-9245 | biostudies-arrayexpress

ATAC-seq of mouse embryonic stem cells

Project description:ATAC-seq of mouse embryonic stem cells

| PRJEB39030 | ENA

A PLURIPOTENT STEM CELL PLATFORM FOR IN VITRO SYSTEMS GENETICS STUDIES OF MOUSE DEVELOPMENT [ATAC-seq]

Project description:The directed differentiation of pluripotent stem cells (PSCs) from panels of genetically diverse individuals is emerging as a powerful experimental system for characterizing the impact of natural genetic variation on developing cell types and tissues. Here, we establish new PSC lines and experimental approaches for modeling embryonic development in a genetically diverse, outbred mouse stock (Diversity Outbred mice). We show that a range of inbred and outbred PSC lines can be stably maintained in the primed pluripotent state (epiblast stem cells) and establish the contribution of genetic variation to phenotypic differences in gene regulation and directed differentiation. Using pooled in vitro fertilization, we generate and characterize a genetic reference panel of Diversity Outbred PSCs (n = 250). Finally, we demonstrate the feasibility of pooled culture of genetically diverse PSCs as “cell villages”, which can facilitate the differentiation of large numbers for forward genetic screens. These data can complement and inform similar efforts within the stem cell biology and human genetics communities to model the impact of natural genetic variation on phenotypic variation and disease-risk.

2025-06-21 | GSE270007 | GEO

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