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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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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

| PRJNA512524 | ENA

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

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

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

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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.

2019-11-01 | GSE124572 | GEO

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.

2015-02-25 | E-MTAB-1935 | biostudies-arrayexpress

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

Project description:ChIP-Seq study in human MCF7 and HEPG2 cells using antibodies against CTCF (Millipore, 07-729), STAG1 (abcam, ab4457), RAD21 (abcam, ab992), ERa (santa cruz, sc-543), CEBPa (santa cruz, sc-9314)

2010-05-13 | E-TABM-828 | biostudies-arrayexpress

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

Project description:CTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in mutually exclusive manners in DNA binding and transcriptional regulation. Here we show that these two proteins co-occupy a specific subset of regulatory elements consisting of clustered CTCF binding motifs (termed 2xCTSes). BORIS occupancy at 2xCTSes is largely invariant in BORIS-positive cancer cells, with the genomic pattern recapitulating the germline-specific BORIS binding to chromatin. In contrast to the single-motif CTCF target sites (1xCTSes), the 2xCTS elements are preferentially found at active promoters and enhancers, both in cancer and germ cells. 2xCTSes are also enriched in genomic regions that escape histone to protamine replacement in human and mouse sperm. Depletion of BORIS gene leads to altered transcription of a large number of genes and the differentiation of K562 cells, while the ectopic expression of this CTCF paralog leads to specific changes in transcription in MCF7 cells. In summary, we discover two functionally and structurally different classes of CTCF binding regions, 2xCTSes and 1xCTSes, revealed by their predisposition to bind BORIS. We propose that 2xCTSes play key roles in the transcriptional program of cancer and germ cells Genome-wide mapping of CTCF and BORIS occupancies in both germ and cancer cells. ChIP-seq and expression profiling by high throughput sequencing

2015-07-23 | E-GEOD-70764 | biostudies-arrayexpress

A screen for cis-regulatory elements for murine miR-142 using an sgRNA library prepared by Molecular Chipper technology

Project description:CRISPR-based loss-of-function screens have been proven powerful to identify genetic regulators in mammalian cells, but current approaches for single guide RNA (sgRNA) library construction are expensive and difficult to be adapted in most laboratories. Here, we present a Molecular Chipper technology for inexpensive and easily customizable sgRNA library generation, and a proof-of-principle screen that identifies novel cis-regulatory regions for miR-142 biogenesis. This method will be useful for functional interrogation of non-coding elements in mammalian genomes

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

2015-07-23 | GSE70764 | GEO