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ATAC-seq in HUDEP-2 cells

ABSTRACT: ATAC-seq in HUDEP-2 cells

PROVIDER: PRJNA704100 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13766495_1.fastq.gz	Fastqsanger.gz
	SRR13766495_2.fastq.gz	Fastqsanger.gz
	SRR13766496_1.fastq.gz	Fastqsanger.gz
	SRR13766496_2.fastq.gz	Fastqsanger.gz
	SRR13766497_1.fastq.gz	Fastqsanger.gz

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ATAC-seq in HUDEP-2 cells

Project description:ATAC-seq was performed in HUDEP-2 cells grown in expansion phase medium following the OMNI-ATAC protocol (Corces MR, et al. Nat. Methods, 2017).

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Modelling of Red Blood Cell Trait GWAS Variants in HUDEP-2 Cells (ATAC-seq)

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Chromosomal loop engineering in human beta globin locus (ATAC-Seq)

Project description:We have engineered the 3 prime HS1 CTCF binding site at the human beta globin gene locus in HUDEP-2 cells and performed RNA-seq/ChIP-seq/ATAC-seq as well as HiC and capture HiC to dissect its potential in regulating gene expression

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Modelling of Red Blood Cell Trait GWAS Variants in HUDEP-2 Cells (ATAC-seq)

Project description:Genome Wides Association Studies (GWAS) have identified tens of thousands of associations between human genetic variation and common disease. Despite the abundance of GWAS associations, functional identification and characterization of causative variants and effector genes remains a challenging prospect. Human erythropoiesis provides a highly tractable model system for the development of tools for GWAS analysis. Using the Human Umbilical Derived Erythroid Progenitor 2 (HUDEP-2) cell line we have modelled the effects of two variants associated with red blood cell traits using CRISPR/Cas9 facilitated HDR editing.

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Genome-wide ZNF410 binding sites identified by CUT&RUN in HUDEP-2, human CD34+ HSPCs and MEL cells.

Project description:We examined the chromatin occupancy of ZNF410 by conducting CUT&RUN. We used an HA antibody to probe for epitope tagged ZNF410 in HUDEP-2 cells. We used a ZNF410 antibody to probe for endogenous ZNF410 in HUDEP-2 cells, human CD34+ hematopoietic stem and progenitor cell (HSPC) derived erythroid precursors and mouse erythroleukemia (MEL) cells.

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ATAC-seq for L3.6pl cells

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Project description:ATAC-seq open chromatin maps for HepG2 cells (3 biological replicates), a liver model.

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Gene expression profiling of HUDEP-2 cells edited with either ZNF410 targeting or control sgRNA

Project description:RNA sequencing was performed of HUDEP-2 cells edited at either ZNF410 or AAVS1 (control locus) to measure gene expression changes due to loss of ZNF410 expression. CHD4 was the most significantly downregulated gene upon ZNF410 editing. We observed that ZNF410 binds to DNA upstream of the CHD4 gene. To test the requirement of ZNF410 binding for CHD4 expression we generated a HUDEP-2 clone in which this region of ZNF410 binding was deleted (CHD4 6.7 kb element deletion clone). We performed RNA-seq of CHD4 6.7 kb element deleted HUDEP-2 cells after either ZNF410 or AAVS1 (control locus) editing and only observed 2 differentially expressed genes after ZNF410 editing in CHD4 6.7 kb element deletion cells, consistent with our results that nearly all gene expression changes found after ZNF410 editing are due to changes in CHD4 expression.

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