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Homo sapiens

ABSTRACT: Epigenome Editing by CRISPR/Cas9 Repressors for Silencing of Distal Regulatory Elements

PROVIDER: PRJNA291509 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2135620_1.fastq.gz	Fastqsanger.gz
	SRR2135620_2.fastq.gz	Fastqsanger.gz
	SRR2135630_1.fastq.gz	Fastqsanger.gz
	SRR2135630_2.fastq.gz	Fastqsanger.gz
	SRR2135621_1.fastq.gz	Fastqsanger.gz

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Homo sapiens

Project description:Epigenome Editing by CRISPR/Cas9 Repressors for Silencing of Distal Regulatory Elements

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CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome [CERES]

Project description:Large genome mapping consortia and thousands of genome-wide association studies have identified non-protein coding elements in the genome as a having a central role in tissue development, cell-type specification, response to environmental or pharmacologic signals, and susceptibility to most common diseases. However, decoding the function of the millions of putative regulatory elements discovered in these studies remains a primary challenge. New CRISPR/Cas9-based epigenome editing technologies have enabled the precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR/Cas9-based Epigenomic Regulatory Element Screening (CERES) for high-throughput screening of regulatory element activity within the native genomic context. We perform both loss- and gain-of-function screens with complementary epigenome editing tools to identify known and unknown regulatory elements of medically relevant genes in human cells. The high-throughput functional annotation of putative regulatory elements by CERES constitutes a new platform for screening biological mechanisms that cannot be perturbed by traditional methods.

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CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome [SKBR3 DNase]

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CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome

Project description:This SuperSeries is composed of the SubSeries listed below. Large genome mapping consortia and thousands of genome-wide association studies have identified non-protein coding elements in the genome as a having a central role in tissue development, cell-type specification, response to environmental or pharmacologic signals, and susceptibility to most common diseases. However, decoding the function of the millions of putative regulatory elements discovered in these studies remains a primary challenge. New CRISPR/Cas9-based epigenome editing technologies have enabled the precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR/Cas9-based Epigenomic Regulatory Element Screening (CERES) for high-throughput screening of regulatory element activity within the native genomic context. We perform both loss- and gain-of-function screens with complementary epigenome editing tools to identify known and unknown regulatory elements of medically relevant genes in human cells. The high-throughput functional annotation of putative regulatory elements by CERES constitutes a new platform for screening biological mechanisms that cannot be perturbed by traditional methods.

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Homo sapiens

Project description:CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome [CERES]

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Project description:CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome [SKBR3 DNase]

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CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome

Project description:CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome

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miRNA-seq of HEK293 cell lines on Illumina iSeq100 instrument

Project description:A validation experiment performed on HEK293 cell lines after genome editing. The design contains three duplicate runs consisted of: HEK293 wild type cell line HEK293 with MIR484 gene knockdown using CRISPR-Cas9 HEK293 with MIR185 gene knockout using CRISPR-Cas9

2023-06-16 | E-MTAB-13009 | biostudies-arrayexpress

A multi-functional AAV-CRISPR-Cas9 and its host response

Project description:CRISPR-Cas9 delivery by AAV holds promise for gene therapy but faces critical barriers due to its potential immunogenicity and limited payload capacity. Here, we demonstrate genome engineering in postnatal mice using AAV-split-Cas9, a multi-functional platform customizable for genome-editing, transcriptional regulation, and other previously impracticable AAV-CRISPR-Cas9 applications. We identify crucial parameters that impact efficacy and clinical translation of our platform, including viral biodistribution, editing efficiencies in various organs, antigenicity, immunological reactions, and physiological outcomes. These results reveal that AAV-CRISPR-Cas9 evokes host responses with distinct cellular and molecular signatures, but unlike alternative delivery methods, does not induce detectable cellular damage in vivo. Our study provides a foundation for developing effective genome therapeutics mRNA-Seq from muscles (9 samples; 3 mice x 3 conditions) and lymph nodes (9 samples; 3 mice x 3 conditions).

2016-07-29 | E-GEOD-84534 | biostudies-arrayexpress

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