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

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

PROVIDER: PRJNA512525 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8384730.fastq.gz	Fastqsanger.gz
	SRR8384731.fastq.gz	Fastqsanger.gz
	SRR8384732.fastq.gz	Fastqsanger.gz
	SRR8384733.fastq.gz	Fastqsanger.gz
	SRR8384734.fastq.gz	Fastqsanger.gz

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

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

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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.

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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.

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ChIP-chip of H3K4Me1, H3K4Me3, H3K4Ac, H3K9Ac, H3K9Me2, H3K27Me3, CTCF and HP1a in MCF7 breast cancer cells

Project description:We report the high-throughput profiling of histone modifications, CTCF and HP1a binding sites in MCF7 breast cancer cells. ChIP-chip experiments were performed using the Agilent Human Genome CGH Microarray 1x1M. Regulatory markers H3K4Me1, H3K4Me3, H3K4Ac, H3K9Ac, CTCF are known to be positively correlated with gene expression, and H3K9Me2, H3K27Me3 and HP1a are negative markers. Together with MCF7 methylation data, we showed hypomethylated promoters are significantly enriched with positive regulatory elements, and lacks repressive markers.

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-11-01 | GSE124575 | GEO

ChIP-Seq of human MCF7 and HEPG2 cells using antibodies against CTCF, STAG1, RAD2, ERa and CEBPa

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Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions

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