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

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

PROVIDER: PRJNA699609 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13634081.fastq.gz	Fastqsanger.gz
	SRR13634082.fastq.gz	Fastqsanger.gz
	SRR13634083.fastq.gz	Fastqsanger.gz
	SRR13634084.fastq.gz	Fastqsanger.gz
	SRR13634085.fastq.gz	Fastqsanger.gz

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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.

2021-02-05 | GSE166222 | GEO

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.

2021-02-05 | GSE166221 | GEO

RNA-seq on MCF7 cells induced with sgRNA vectors targeting CTCF binding elements

Project description:We performed a CRISPR-based functional genetic screen targeting CTCF binding elements (CBEs) located in the vicinity of ERα-bound enhancers. The screen identified four functional CBEs whose targeting resulted in a marked negative effect on the proliferation of MCF-7 cells (ERα-positive cells) but no significant effect on MDA-MB-231 (ERα-negative cells) cells. We then carried out RNA-seq analysis on MCF-7 cells induced with sgRNA vectors targeting these four CBEs: sgRNA_1118, sgRNA_1659, sgRNA_680 and sgRNA_810, as well as non-targeting sgRNA as control.

2019-11-01 | GSE124573 | GEO

GRO-seq on MCF7 cells induced with sgRNA vectors targeting CTCF binding elements

Project description:We performed a CRISPR-based functional genetic screen targeting CTCF binding elements (CBEs) located in the vicinity of ERα-bound enhancers. The screen identified four functional CBEs whose targeting resulted in a marked negative effect on the proliferation of MCF-7 cells (ERα-positive cells) but no significant effect on MDA-MB-231 (ERα-negative cells) cells. Here, we carried out GRO-seq analysis on MCF-7 cells induced with an sgRNA vector targeting one of the hits detected by the screen: sgRNA_1118, as well as non-targeting sgRNA and sg1830 as control.

2019-11-01 | GSE124572 | GEO

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

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

| PRJNA699604 | ENA

ZNF410 uniquely activates the NuRD component CHD4 to silence fetal hemoglobin expression [RNA-Seq]

Project description:Metazoan transcription factors typically regulate large numbers of genes. Here we identify via a CRISPR-Cas9 genetic screen ZNF410, a pentadactyl DNA binding protein that in human erythroid cells directly and measurably activates only one gene, the NuRD component CHD4. Specificity is conveyed by two highly evolutionarily conserved clusters of ZNF410 binding sites near the CHD4 gene with no counterparts elsewhere in the genome. Loss of ZNF410 in adult type human erythroid cell culture systems and xenotransplant settings diminishes CHD4 levels and derepresses the fetal hemoglobin genes. While previously known to be silenced by CHD4, the fetal globin genes are exposed here as among the most sensitive to reduced CHD4 levels. In vitro DNA binding assays and crystallographic studies reveal the ZNF410-DNA binding mode. ZNF410 is a remarkably selective transcriptional activator in erythroid cells whose perturbation might offer new therapeutic opportunities in the treatment of hemoglobinopathies.

2020-12-09 | GSE154961 | GEO

ZNF410 uniquely activates the NuRD component CHD4 to silence fetal hemoglobin expression [ChIP-Seq]

2020-12-09 | GSE154960 | GEO

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ATAC-seq in HUDEP-2 cells

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2021-02-23 | GSE167298 | GEO

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