Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

NG Capture-C from human erythroid and embryonic stem cells

ABSTRACT: NG Capture-C provides high resolution chromatin conformation capture (3C) interaction maps. NG Capture-C was carried out in erythroid and hESC cells at the Hba, Hbb, Myc, and Slc25a37 locus to generate sequence libraries for analytical software testing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE129378 | GEO | 2020/11/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Targeted high-resolution chromosome conformation capture at genome-wide scale in mouse erythroid cells

Project description:Chromosome conformation capture (3C) provides an adaptable tool through which to study diverse biological questions. Currently, 3C techniques provide either low-resolution interaction profiles across the entire genome, e.g. HiC, or high-resolution interaction profiles at up to several hundred loci, e.g. NG Capture-C and 4C-seq. Generation of high-resolution, genome-wide interaction profiles can feasibly be achieved through efficiency improvements to current high-resolution methods. To this end we systematically tested and removed areas inefficiency in NG Capture-C to develop a new method Nuclear Capture-C, which provides a 300% increase in informative sequencing content. Using Nuclear Capture-C we target 8,026 erythroid promoters in triplicate, showing that this method can achieve high-resolution genome-wide 3C interaction profiles at scale.

2020-10-28 | GSE160229 | GEO

NG Capture-C from human erythroid and embryonic stem cells

Project description:NG Capture-C from human erythroid and embryonic stem cells

| PRJNA531102 | ENA

Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin accessibility and looping [RNA-Seq 2]

Project description:During the human cord blood CD34+ cell differentiation, expression of the genes which contribute to erycyte maturation are increased, inculding ALAS2, SLC25A37, GYPA and KLF1. ETO2 functions as a transcription repressor and is required for the erythrocyte maturation and the hemoglobin switch. During mouse embryonic erythropoiesis, RNA-seq data in E8.5 yolk sac /E12.5, E14.5 fetal liver cells indicated that eto2 promoted a critical developmental transition and played an important role in globin switch from embryonic to adult β-globin transcription since its function is essential for erythorid maturation regulators (Alas2,Slc25a37,Epb42,Gypc,Klf1) and globin genes (Hbb-y and Hba-x) regulation.

2020-08-25 | GSE156306 | GEO

NG Capture-C analysis of GADD45a-bound adipogenic super-enhancers

Project description:ING1b and GADD45a are nuclear proteins involved in the regulation of cell growth, apoptosis and DNA repair. We previously found that ING1b is essential to target GADD45a-mediated active DNA-demethylation via TET1 to specific loci. In order to study the physical interaction of distant GADD45a and ING1 bound regions, we performed multiplexed NG Capture-C chromatin conformation capture assay in wildtype and knockout mouse embryonic fibroblasts.

2018-06-11 | GSE99606 | GEO

Characterisation by Next generation Capture-C of Pax6 locus in a mouse cell line with bleomycin treatment to relieve topological stress

Project description:NG-Capture-C profiling of chromatin interactions (using DpnII 3C and Oligo nucleotide sequence capture followed by Next generation sequencing) of enhancers, promoters and CTCF/Rad21 binding sites throughout a ~600kb region of the mouse Pax6 locus in β-TC3 cells treated with alpha amanitin. β-TC3 cell are a mouse pancreatic β cell derived from mouse insulinoma.

2023-06-21 | GSE235335 | GEO

Characterisation by Next generation Capture-C of Pax6 locus in a mouse cell line with alpha amanatin treatment to inhibit transcription

2023-06-21 | GSE235334 | GEO

Characterisation of chromatin states in erythroid cells from a patient with a unique severe HbH genotype (NG Capture C)

Project description:Analyses of mutations within the a-globin cluster which downregulate a-globin expression and cause a-thalassaemia provide the basis for genetic counselling and pre-natal diagnosis of this common form of anemia. Understanding the mechanisms by which such mutations cause a-thalassemia has established many of the principles by which mammalian genes are regulated and how this goes awry in human genetic disease. ATAC-Seq and NG Capture-C data from an individual (NSE) with a unique a-globin genotype involving a deletion of the main alpha-globin enhancer on one allele and the --/SEA mutation on the other help to address how the human a-globin cluster is normally regulated.

2022-05-06 | GSE149793 | GEO

Project description:Precisely co-ordinated activation of lineage specific transcription factors direct cell fate decisions during mouse early development. The T-box transcription factor Eomes is dynamically expressed during mouse gastrulation and is a key regulator of the anterior visceral endoderm (AVE), cardiac mesoderm and definitive endoderm (DE) lineages. The cis-acting regulatory elements that direct spatiotemporally restricted Eomes expression domains have yet to be elucidated. To understand transcriptional regulation of Eomes in Definitive Endoderm open chromatin data was generated by ATAC-seq and histone modifications identified by ChIP-seq. Interactions at the Eomes locus and the loci of two related transcription factors Foxa2 and Lhx1, was also determined by NG Capture-C.

2017-01-30 | GSE94051 | GEO

Characterisation by Next generation Capture-C of Pax6 locus in three mouse cell lines (MV+, RAG and β-TC3 cells).

Project description:NG-Capture-C profiling of chromatin interactions (using DpnII 3C and Oligo nucleotide sequence capture followed by Next generation sequencing) of enhancers, promoters and CTCF/Rad21 binding sites throughout a ~600kb region of the mouse Pax6 locus in three expression states, High (β-TC3), On (MV+) and OFF (RAG). β-TC3 cell are a mouse pancreatic β cell derived from mouse insulinoma, MV+ a lens epithelium cell line and RAG a mouse kidney adenocarcinoma cell line.

2018-10-18 | GSE120666 | GEO

NG-Capture C analysis of 35 gene loci regulated by Fra-1 in MDA-MB-231 cells

Project description:In the article "Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers" by Bejjani et al., we used NG Capture-C approach to identify regulatory elements interacting with the promoters of 35 Fra-1 regulated genes in the triple negative breast cancer cell line MDA-MB-231

2021-02-23 | GSE146824 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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