Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin landscapes in mouse haploid stem cells [ChIP-seq]

ABSTRACT: Chromatin landscapes in mouse haploid stem cells [ChIP-seq]

PROVIDER: PRJNA419892 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6324125_1.fastq.gz	Fastqsanger.gz
	SRR6324125_2.fastq.gz	Fastqsanger.gz
	SRR6324126_1.fastq.gz	Fastqsanger.gz
	SRR6324126_2.fastq.gz	Fastqsanger.gz
	SRR6324127_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Chromatin landscapes in mouse haploid stem cells [ChIP-seq]

Project description:We generate histone modification profiles and DNA methylation profiles of mouse haploid embryonic stem cells. By comparison to mouse diploid ESCs and MEFs, we found the similar chromatin landscapes between haESCs and mESCs, which reveal the self-renew ability and pluripotency in haESCs. Besides, haESCs specific chromatin landscapes show its sperm-like functions.

2018-03-07 | GSE107358 | GEO

Chromatin landscapes in mouse haploid stem cells

Project description:Chromatin landscapes in mouse haploid stem cells

| PRJNA419887 | ENA

Chromatin landscapes in mouse haploid stem cells [RRBS-seq]

2018-03-07 | GSE107359 | GEO

Chromatin landscapes in mouse haploid stem cells [RRBS-seq]

Project description:Chromatin landscapes in mouse haploid stem cells [RRBS-seq]

| PRJNA419891 | ENA

Chromatin landscapes in mouse haploid stem cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-03-07 | GSE107360 | GEO

CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [ChIP-Seq]

Project description:CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [ChIP-Seq]

| PRJNA490592 | ENA

ChIP-MS reveals the local chromatin composition by label-free quantitative proteomics

Project description:Chromatin immunoprecipitation (ChIP) has been a cornerstone for epigenetic analyses over the last decades, but even coupled to sequencing approaches (ChIP-seq), it is ultimately limited to one protein at a time. In a complementary effort, we here combined ChIP with label-free quantitative (LFQ) mass spectrometry (ChIP-MS) to interrogate local chromatin compositions. We demonstrate the versality of our approach at telomeres, with transcription factors, in tissue and by dCas9-driven locus-specific enrichment.

2024-03-05 | PXD039701 | Pride

ChIP-MS reveals the local chromatin composition by label-free quantitative proteomics

2024-03-05 | PXD039627 | Pride

Haploid embryonic stem cells

Project description:Mammalian haploid embryonic stem cells (haESCs) provide new possibilities for large-scale genetic screens because they bear only one copy of each chromosome. However, haESCs are prone to spontaneous diploidization through unknown mechanisms. Here, we report that a small molecule combination could restrain mouse haESCs from diploidization by impeding exit from naïve pluripotency and by shortening the S-G2/M phases. Combined with 2i and PD166285, our chemical cocktail could maintain haESCs in the haploid state for at least five weeks without fluorescence-activated cell sorting (FACS) enrichment of haploid cells. Taken together, we established an effective chemical approach for long-term maintenance of haESCs, and highlighted that proper cell cycle progression was critical for the maintenance of haploid state.

2017-10-31 | GSE104519 | GEO

Transcriptome profiles and chromatin states in mouse androgenetic haploid embryonic stem cells.

Project description:Haploid embryonic stem cells (haESCs) are derived from the inner cell mass of the haploid blastocyst, containing only one set of chromosomes. Extensive and accurate chromatin remodelling occurs during haESC derivation, but the intrinsic transcriptome profiles and chromatin structure of haESCs have not been fully explored. We profiled the transcriptomes, nucleosome positioning, and key histone modifications of four mouse haESC lines, and compared these profiles with those of other closely-related stem cell lines, MII oocytes, round spermatids, sperm, and mouse embryonic fibroblasts. haESCs had transcriptome profiles closer to those of naïve pluripotent stem cells. Consistent with the one X chromosome in haESCs, Xist was repressed, indicating no X chromosome inactivation. haESCs and ESCs shared a similar global chromatin structure. However, a nucleosome depletion region was identified in 2056 promoters in ESCs, which was absent in haESCs. Furthermore, three characteristic spatial relationships were formed between transcription factor motifs and nucleosomes in both haESCs and ESCs, specifically in the linker region, on the nucleosome central surface, and nucleosome borders. Furthermore, the chromatin state of 4259 enhancers was off in haESCs but active in ESCs. Functional annotation of these enhancers revealed enrichment in regulation of the cell cycle, a predominantly reported mechanism of haESC self-diploidization. Notably, the transcriptome profiles and chromatin structure of haESCs were highly preserved during passaging but different from those of differentiated cell types.

| S-EPMC10472531 | biostudies-literature

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