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Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (4C-Seq)

ABSTRACT: Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (4C-Seq)

PROVIDER: PRJNA490760 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7828100.fastq.gz	Fastqsanger.gz
	SRR7828110.fastq.gz	Fastqsanger.gz
	SRR7828101.fastq.gz	Fastqsanger.gz
	SRR7828111.fastq.gz	Fastqsanger.gz
	SRR7828102.fastq.gz	Fastqsanger.gz

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Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (4C-Seq)

Project description:Cis Regulatory Elements (CREs) regulate the expression of the genes in their genomic neighborhoods and influence cellular processes such as cell-fate maintenance and differentiation. To date, there remain major gaps in the functional characterization of CREs and the identification of its target genes in the cellular native environment. In this study, we performed a Features Oriented CRISPR Utilized Systematic (FOCUS) screen of Oct4-bound CREs using CRISPR/Cas9 to identify functional CREs important for pluripotency maintenance in mouse ES cells.

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Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen

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Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (ChIP-Seq)

Project description:Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (ChIP-Seq)

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Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (ChIP-Seq)

2020-09-13 | GSE131644 | GEO

Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (RNA-Seq 2)

2020-09-13 | GSE119950 | GEO

Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (RNA-Seq 1)

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Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (RNA-Seq 1)

Project description:Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (RNA-Seq 1)

| PRJNA490762 | ENA

Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (RNA-Seq 2)

Project description:Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (RNA-Seq 2)

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Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen

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

2020-09-13 | GSE119951 | GEO

CTCF binding polarity determines chromatin looping [4C]

Project description:CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional organization of chromatin. In this study, we systematically assayed the 3D genomic contact profiles of hundreds of CTCF binding sites in multiple tissues with high-resolution 4C-seq. We find both developmentally stable and dynamic chromatin loops. As recently reported, our data also suggest that chromatin loops preferentially form between CTCF binding sites oriented in a convergent manner. To directly test this, we used CRISPR-Cas9 genome editing to delete core CTCF binding sites in three loci, including the CTCF site in the Sox2 super-enhancer. In all instances, CTCF and cohesin recruitment were lost, and chromatin loops with distal CTCF sites were disrupted or destabilized. Re-insertion of oppositely oriented CTCF recognition sequences restored CTCF and cohesin recruitment, but did not re-establish chromatin loops. We conclude that CTCF binding polarity plays a functional role in the formation of higher order chromatin structure. 4C-seq was performed on a large number of viewpoints in E14 embryonic stem cells, neural precursor cells and primary fetal liver cells

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