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NG Capture-C from human erythroid and embryonic stem cells

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

PROVIDER: PRJNA531102 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8858530_1.fastq.gz	Fastqsanger.gz
	SRR8858530_2.fastq.gz	Fastqsanger.gz
	SRR8858531_1.fastq.gz	Fastqsanger.gz
	SRR8858531_2.fastq.gz	Fastqsanger.gz
	SRR8858532_1.fastq.gz	Fastqsanger.gz

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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.

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Metabolomics Workbench ST000003 - GNPS - Metabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells

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

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Multiplexed Chromatin Conformation Capture in Mouse Erythroid cells using Capture-C

Project description:Multiplexed Chromatin Conformation Capture in Mouse Erythroid cells , from hundreds of targeted loci, using agilent oligo capture technology and high throughput sequencing. Two erythroid Ter119+ cell replicates and a mouse ES cell control

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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.

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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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Multiplexed Chromatin Conformation Capture in Mouse Erythroid cells using Capture-C

Project description:Multiplexed Chromatin Conformation Capture in Mouse Erythroid cells , from hundreds of targeted loci, using agilent oligo capture technology and high throughput sequencing.

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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.

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2023-05-05 | PXD025194 | Pride

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