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

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

PROVIDER: PRJNA630166 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11684061_1.fastq.gz	Fastqsanger.gz
	SRR11684061_2.fastq.gz	Fastqsanger.gz
	SRR11684062_1.fastq.gz	Fastqsanger.gz
	SRR11684062_2.fastq.gz	Fastqsanger.gz
	SRR11684063_1.fastq.gz	Fastqsanger.gz

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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

NG Capture-C from human erythroid and embryonic stem cells

Project description: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.

2020-11-02 | GSE129378 | GEO

Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [NG Capture-C]

Project description:Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [NG Capture-C]

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NG Capture-C from human erythroid and embryonic stem cells

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

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Characterisation of chromatin states in erythroid cells from a patient with a unique severe HbH genotype

Project description:Characterisation of chromatin states in erythroid cells from a patient with a unique severe HbH genotype

| PRJNA630165 | ENA

Characterisation of chromatin states in erythroid cells from a patient with a unique severe HbH genotype (ATAC-Seq)

Project description:Characterisation of chromatin states in erythroid cells from a patient with a unique severe HbH genotype (ATAC-Seq)

| PRJNA630167 | ENA

Characterisation of chromatin states in erythroid cells from a patient with a unique severe HbH genotype (ATAC-Seq)

2022-05-06 | GSE149794 | GEO

Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [NG Capture-C]

Project description:Mammalian genomes are subdivided into large (50-2000 kb) regions of chromatin referred to as Topologically Associating Domains (TADs or sub-TADs). Chromatin within an individual TAD contacts itself more frequently than with regions in surrounding TADs thereby directing enhancer-promoter interactions. In many cases, the borders of TADs are defined by convergently orientated boundary elements associated with CCCTC-binding factor (CTCF), which stabilises the cohesin complex on chromatin and prevents its translocation. This delimits chromatin loop extrusion which is thought to underlie the formation of TADs. However, not all CTCF-bound sites act as boundaries and, importantly, not all TADs are flanked by convergent CTCF sites. Here, we examined the CTCF binding sites within a ~70 kb sub-TAD containing the duplicated mouse α-like globin genes and their five enhancers (5’-R1-R2-R3-Rm-R4-α1-α2-3’). The 5’ border of this sub-TAD is defined by a pair of CTCF sites. Surprisingly, we show that deletion of the CTCF binding sites within and downstream of the α-globin locus leaves the sub-TAD largely intact. The predominant 3’ border of the sub-TAD is defined by a steep reduction in contacts: this corresponds to the transcribed α2-globin gene rather than the CTCF sites at the 3’-end of the sub-TAD. Of interest, the almost identical α1- and α2-globin genes interact differently with the enhancers, resulting in preferential expression of the proximal α1-globin gene which behaves as a partial boundary between the enhancers and the distal α2-globin gene. Together, these observations provide direct evidence that actively transcribed genes can behave as boundary elements.

2022-06-01 | GSE153208 | GEO

Scalable Production of Mouse Erythroid Cells using an in vitro Embryoid Body differentiation System [Capture-C]

Project description:Mouse embryonic stem (mES) cells can be manipulated ex-vivo to recapitulate the process of erythropoiesis, whereby multipotential haematopoietic stem cells undergo lineage specification, differentiation and maturation to produce functional erythroid cells. Although very useful for identifying specific progenitors and precursors, this cell system has not been fully exploited as a source of cells to analyse erythropoiesis, compared with primary erythroid cells or immortalised cell lines. Here we have established a protocol in which erythroid cells can be isolated in a scalable manner from differentiated embryoid bodies (EBs). Using transcriptional and epigenetic analysis, we show that all purified erythroid cells in this system are derived from the primitive haematopoietic lineage. Finally, we show that this system faithfully recapitulates normal erythropoiesis in the embryonic mouse and fully mimics the effects of natural and engineered mutations seen in full mouse models. Data deposited here comprises chromatin profiling of the EB derived CD71+ erythroid cells; chromatin accessibility (ATAC-Seq), characterisation of the open chromatin by associated histone modifications (ChIP-Seq), chromatin structure (CTCF ChIP-Seq and Capture C interaction data). WT CD71+ cells were compared to either mutant CD71+ cells or other erythroid tissues (mouse adult spleen, E13.5 fetal liver, early embryonic circulating blood) representing both definitve and primitive erythroid lineages.

2021-09-22 | GSE184432 | GEO

Amplified EPOR/JAK2 genes define a unique subtype of acute erythroid leukemia

Project description:Acute erythroid leukemia (AEL) is a unique subtype of acute myeloid leukemia characterized by prominent erythroid proliferation, whose molecular basis is poorly understood. To elucidate the underlying mechanism of erythroid proliferation, we performed comprehensive genomic study. The aim of this study is to unveil genotype phenotype correlations and the feasible molecular targets for therapy of AEL.

| EGAS00001005810 | EGA

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