Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE104579 | GEO | 2017/11/24

SECONDARY ACCESSION(S): PRJNA413130

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [HiC]

Project description:We present the high resolution HiC study of genome folding in primary cells, specifically hematopoietic stem and progenitor cells. We investigated the relationship of chromosomal contacts with other epigenetic marks, particularly DNA methylation and histone modifications which is known to be important for appropriate stem cell differentiation.

2017-11-24 | GSE107148 | GEO

DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [RNA-seq]

Project description:We present the high resolution HiC study of genome folding in primary hematopoietic stem and progenitor cells. We investigated the relationship of chromosomal contacts with other epigenetic marks, particularly DNA methylation which is known to be important for appropriate stem cell differentiation.

2017-11-24 | GSE107149 | GEO

DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [ChIP-seq]

2017-11-24 | GSE107147 | GEO

DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells

Project description:DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells

| PRJNA413130 | ENA

DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [HiC]

Project description:DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [HiC]

| PRJNA419462 | ENA

DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [ChIP-seq]

Project description:DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [ChIP-seq]

| PRJNA419461 | ENA

DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [RNA-seq]

Project description:DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [RNA-seq]

| PRJNA419463 | ENA

Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity.

Project description:Higher-order chromatin structure and DNA methylation are implicated in multiple developmental processes, but their relationship to cell state is unknown. Here, we find that large (>7.3 kb) DNA methylation nadirs (termed "grand canyons") can form long loops connecting anchor loci that may be dozens of megabases (Mb) apart, as well as inter-chromosomal links. The interacting loci cover a total of ∼3.5 Mb of the human genome. The strongest interactions are associated with repressive marks made by the Polycomb complex and are diminished upon EZH2 inhibitor treatment. The data are suggestive of the formation of these loops by interactions between repressive elements in the loci, forming a genomic subcompartment, rather than by cohesion/CTCF-mediated extrusion. Interestingly, unlike previously characterized subcompartments, these interactions are present only in particular cell types, such as stem and progenitor cells. Our work reveals that H3K27me3-marked large DNA methylation grand canyons represent a set of very-long-range loops associated with cellular identity.

| S-EPMC7357281 | biostudies-literature

Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin

Project description:Heterochromatin is a tightly packed form of DNA, which is associated with histone 3 lysine 9 methylation (H3K9me). Here, we identify an H3K9me2 binding protein, Agenet domain (AGD)-containing protein 1 (AGDP1), in Arabidopsis thaliana. Our biochemical studies revealed that the AGDP1 can specifically recognize the H3K9me2 marks by the three pairs of tandem-AGDs. We determined the crystal structure of the AGD12 of Raphanus sativus AGDP1 in complex with an H3K9me2 peptide. In the complex, the histone peptide adopts a unique helical conformation. AGD12 employs a newly defined interacting interface to specifically recognize the H3K4me0 and H3K9me2 marks. In addition, we found that AGDP1 is required for transcriptional gene silencing, non-CG DNA methylation, and H3K9 dimethylation. Our ChIP-seq data showed that AGDP1 is enriched in TE regions and associated with the heterochromatin marks. Our findings suggest that, as a heterochromatin binding protein, AGDP1 links H3K9me2 to DNA methylation in heterochromatin regions.

2018-10-23 | GSE111609 | GEO

DNA methylation profiles of human hematopoietic progenitors [BLUEPRINT hematopoietic progenitors]

Project description:An optimized whole genome bisulfite sequencing protocol (µWGBS, Farlik et al. 2015 Cell Reports) was used to establish DNA methylation profiles of FACS-purified stem and progenitor cells types of the human blood lineage. Most cell types were sorted from the peripheral blood of three donors each (43 donors total) with eight pools of ten cells, two pools of 50 cells, and one pool of 1000 cells. Additionally, two cell types (HSC, MPP) were sorted from bone marrow, fetal liver, and cord blood; single-cell methylome sequencing (scWGBS, Farlik et al. 2015 Cell Reports) was done for selected cell types (HSC, MPP, CMP, GMP, CLP, MLP0); and gene expression profiling using the Smart-seq2 protocol (Picelli et al. 2013 Nature Methods) was done on all stem/progenitor cell types (HSC, MPP, CMP, MEP, GMP, CLP, MLP0, MLP1, MLP2, MLP3).

2016-11-06 | GSE87196 | 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