Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide maps of Trim33, Ctcf and H3K27ac binding in embryoid bodies

ABSTRACT: Genome-wide maps of Trim33, Ctcf and H3K27ac binding in embryoid bodies

PROVIDER: PRJNA490537 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7823321.fastq.gz	Fastqsanger.gz
	SRR7823322.fastq.gz	Fastqsanger.gz
	SRR7823323.fastq.gz	Fastqsanger.gz
	SRR7823324.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Genome-wide maps of Trim33, Ctcf and H3K27ac binding in embryoid bodies

Project description:We report high throughput profiling and co-occupancy of Trim33, Ctcf and H3K27ac in differentiating embryoid bodies derived from mouse embryonic stem cells. An average of ~37 million reads were generated for each of the described samples and input sample generating 4,426, 52,446, 30,047 peaks respectively for Trim33, CTCF and H3K27ac. Motif enrichment analyses for Trim33 ChiP-Seq data returned CTCF and BORIS (CTCF analog) motifs as best matches. Of the merged peaks, 723 were shared by Trim33, CTCF as well as H3K27ac. In addition, 1299 peaks were shared by Trim33 and CTCF, 1131 were shared by Trim33 and H3K27ac and 3321 were shared by CTCF and H3K27ac.

2019-01-01 | GSE119874 | GEO

Expression data from Mst knockout embryoid bodies and wild type embryoid bodies

Project description:Mst1/Mst2 are central components of Hippo pathway. We examined the role of Mst1/Mst2 in ES cell differentiation. In this data set, we include expression data from day 4 and day 8 Mst1/Mst2 knockout ES cell formed embryoid bodies and wild type embryoid body controls.

2014-01-02 | GSE50219 | GEO

Expression data from Mst knockout embryoid bodies and wild type embryoid bodies

2014-01-02 | E-GEOD-50219 | biostudies-arrayexpress

Embryoid Bodies from Mouse R1 ES - 9 day

Project description:Embryoid Bodies from Mouse R1 ES - 9 day Keywords: other

2005-07-28 | GSE3007 | GEO

Bulk RNAseq of differentiation timecourse of embryoid bodies

Project description:Bulk RNAseq of differentiation timecourse of embryoid bodies from KOLF2.2J AAVS1 inducible CRISPRi lines

2025-02-03 | GSE288399 | GEO

Genome-wide maps of Rad21 in R1/E embryonic stem cells and R1/E derived Embryoid bodies

Project description:ChIP-seq based determination of Rad21 binding sites in embryonic stem cells (ESC) and ESC derived Embryoid Bodies (EB) identified

2011-05-19 | GSE24029 | GEO

Recruitment of TRIM33 to cell-context specific PML nuclear bodies regulates Nodal signaling in mESCs

Project description:TRIM33 is a chromatin reader required for mesendoderm differentiation upon activation of Nodal signaling. But, its role in mESCs is still elusive. Here, we found that TRIM33 co-localizes with promyelocytic leukemia nuclear bodies (PML NBs) specifically in mESCs to mediate Nodal signaling-directed transcription of Lefty1/2. We showed that TRIM33 puncta formation in mESCs depends on PML and specific assembly of PML NBs. Moreover, TRIM33 and PML co-regulate Lefty1/2 expression in mESCs. In addition, both PML and mESCs-specific PML NBs are required for TRIM33 recruitment at Lefty1/2 loci. Remarkably, PML NBs directly associate with the Lefty1/2 loci in mESCs. Finally, a TurboID proximity labeling experiment confirmed that TRIM33 is highly enriched in the mESCs-specific PML NBs. Thus, our study provides the mechanistic insight about TRIM33 condensate in regulating Nodal signaling-directed transcription in mESCs, it also reveals that PML NBs recruit distinct sets of client proteins in cell context dependent manner.

2022-12-08 | GSE199738 | GEO

Trim33 regulates early maturation of mouse embryoid bodies in vitro.

Project description:Embryonic stem cells (ESCs) are an established model for investigating developmental processes, disease conditions, tissue regeneration and therapeutic targets. Previous studies have shown that tripartite motif-containing 33 protein (Trim33) functions as a chromatin reader during Nodal-induced mesoderm induction. Here we report that despite reduced proliferation, mouse ESCs deficient in Trim33 remained pluripotent when cultured under non-differentiating conditions. However, when induced to differentiate to embryoid bodies (EBs), the mutant cultures showed increased cell shedding and apoptosis at day 3 of differentiation. Gene set enrichment analysis (GSEA) indicated that several molecular functions associated with cell survival, transcriptional/translational activity and growth factor signaling were affected already by the second day of differentiation in Trim33-deficient EBs. Consistent with increased apoptosis, expression of Rac1, a critical factor for EB cell survival, was reduced in Trim33 mutant EBs. In addition, a set of genes involved in regulation of pluripotency was upregulated in mutant EBs. Our results suggest that Trim33 regulates early maturation of mouse embryoid bodies in vitro.

| S-EPMC5650645 | biostudies-literature

Genome-wide maps of Rad21 in R1/E embryonic stem cells and R1/E derived Embryoid bodies

Project description:ChIP-seq based determination of Rad21 binding sites in embryonic stem cells (ESC) and ESC derived Embryoid Bodies (EB) identified Examination of Rad21 binding sites in 2 cell types

2011-05-19 | E-GEOD-24029 | biostudies-arrayexpress

Effect of endoglin loss on embryoid bodies

Project description:Analysis of embryonic sten cell-derived embryoid bodies following endoglin knock out. Loss of endoglin leads to profound reduction of key hematopoietic regulators including SCL, LMO2, Gata2, and TGF-β signaling molecule ALK-1. Results provide insight into molecular mechanisms underlying hemangioblast and primitive hematopoietic development.

2011-05-16 | GSE29300 | 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