GEO DataSets

(Submitter supplied) Epigenome editing with the CRISPR/Cas9 platform is a promising technology to modulate gene expression to direct cell phenotype and to dissect the causal epigenetic mechanisms that direct gene regulation. Fusions of the nuclease-inactive dCas9 to the KRAB repressor domain (dCas9-KRAB) can effectively silence target gene expression. We targeted dCas9-KRAB to the HS2 enhancer, a distal regulatory element that orchestrates the expression of multiple globin genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15520 GPL16791

18 Samples

Download data: TXT

(Submitter supplied) Epigenome editing with the CRISPR/Cas9 platform is a promising technology to modulate gene expression to direct cell phenotype and to dissect the causal epigenetic mechanisms that direct gene regulation. Fusions of the nuclease-inactive dCas9 to the KRAB repressor domain (dCas9-KRAB) can effectively silence target gene expression. We targeted dCas9-KRAB to the HS2 enhancer, a distal regulatory element that orchestrates the expression of multiple globin genes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

30 Samples

Download data: BW

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL11154 GPL15520

95 Samples

Download data: NARROWPEAK

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

92 Samples

Download data: XLSX

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

3 Samples

Download data: NARROWPEAK

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Methylation profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20301 GPL21145

15 Samples

Download data: IDAT

(Submitter supplied) Rewriting of the epigenome has risen as a promising alternative to gene editing for precision medicine. In nature, epigenetic silencing can result in complete attenuation of target gene expression over multiple mitotic divisions. However, persistent repression has been difficult to achieve using targeted systems. Here, we report that robust and persistent epigenetic memory required both a DNA methyltransferase (DNMT3A-dCas9) and a histone methyltransferase (Ezh2-dCas9 or KRAB-dCas9). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

7 Samples

Download data: BEDGRAPH, NARROWPEAK

(Submitter supplied) Rewriting of the epigenome has risen as a promising alternative to gene editing for precision medicine. In nature, epigenetic silencing can result in complete attenuation of target gene expression over multiple mitotic divisions. However, persistent repression has been difficult to achieve using targeted systems. Here, we report that robust and persistent epigenetic memory required both a DNA methyltransferase (DNMT3A-dCas9) and a histone methyltransferase (Ezh2-dCas9 or KRAB-dCas9). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

8 Samples

Download data: IDAT, TXT

(Submitter supplied) Epigenetic modifications determine the structure and regulation of eukaryotic genomes and define key signatures of cell lineage specification. Technologies that facilitate the targeted manipulation of epigenetic marks could be used to precisely control cell phenotype or interrogate the relationship between the epigenome and transcriptional control. Here we have generated a programmable acetyltransferase based on the CRISPR/Cas9 gene regulation system, consisting of the nuclease-null dCas9 protein fused to the catalytic core of the human acetyltransferase p300. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL18573

110 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Tissue-specific gene expression requires coordinated control of gene-proximal and distal cis-regulatory elements (CREs), yet functional analysis of putative gene-distal CREs such as enhancers remains challenging. Here we describe enhanced CRISPR/dCas9-based epigenetic editing systems, enCRISPRa and enCRISPRi, for multiplexed analysis of enhancer function in situ and in vivo. Using dual effector proteins capable of re-writing enhancer-associated chromatin modifications, we show that enCRISPRa and enCRISPRi modulate gene transcription by remodeling local epigenetic landscapes at sgRNA-targeted enhancers and associated genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

10 Samples

Download data: TXT

(Submitter supplied) Tissue-specific gene expression requires coordinated control of gene-proximal and distal cis-regulatory elements (CREs), yet functional analysis of putative gene-distal CREs such as enhancers remains challenging. Here we describe enhanced CRISPR/dCas9-based epigenetic editing systems, enCRISPRa and enCRISPRi, for multiplexed analysis of enhancer function in situ and in vivo. Using dual effector proteins capable of re-writing enhancer-associated chromatin modifications, we show that enCRISPRa and enCRISPRi modulate gene transcription by remodeling local epigenetic landscapes at sgRNA-targeted enhancers and associated genes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

99 Samples

Download data: BIGWIG

(Submitter supplied) Tissue-specific gene expression requires coordinated control of gene-proximal and distal cis-regulatory elements (CREs), yet functional analysis of putative gene-distal CREs such as enhancers remains challenging. Here we describe enhanced CRISPR/dCas9-based epigenetic editing systems, enCRISPRa and enCRISPRi, for multiplexed analysis of enhancer function in situ and in vivo. Using dual effector proteins capable of re-writing enhancer-associated chromatin modifications, we show that enCRISPRa and enCRISPRi modulate gene transcription by remodeling local epigenetic landscapes at sgRNA-targeted enhancers and associated genes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

1 Sample

Download data: BIGWIG

(Submitter supplied) Pooled CRISPR-Cas9 screens have recently emerged as a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated. Here, we conducted multiple genome-scale CRISPR screens for essential CTCF loop anchors in the human K562 erythroid cell line. Surprisingly, the primary drivers of apparent ``hits'' in this screen were single guide RNAs (sgRNAs) with low sequence specificity. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

104 Samples

Download data: BEDGRAPH, CSV

(Submitter supplied) Cas9 fused to VP16 repeats have been used in several systems of gene activation. Here we aimed to evaluate the undesirable effects of this system whether in presence or absence of gRNAS targeting a specific gene, CD34.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL16791 GPL20795

17 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Fusion of active protein domains to the nuclease-deficient clustered regularly interspaced short palindromic repeat (CRISPR) associated protein 9 (dCas9) has been widely used for epigenome editing, but the specificities of these engineered proteins have still not been fully investigated. Targeted methylation of specific gene loci offers a direct approach to perturb DNA methylation-associated biological processes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20795

15 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Fusion of active protein domains to the nuclease-deficient clustered regularly interspaced short palindromic repeat (CRISPR) associated protein 9 (dCas9) has been widely used for epigenome editing, but the specificities of these engineered proteins have still not been fully investigated. Targeted methylation of specific gene loci offers a direct approach to perturb DNA methylation-associated biological processes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

2 Samples

Download data: TXT

(Submitter supplied) We report the generation of CRISPR-dCas9 DNA methyltransferases to mediate targeted DNA methylation. Using the dCas9-BFP-DNMT3A and dCas9-BFP-DNMT3B methyltransferases, we have demonstrated that these two methyltransferase can mediate targeted methylation in three human genes tested: uPA, TGFBR3, and CDKN2A in human HEK293T cells. We also showed that these methyltransferases could mediate gene inhibition.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

5 Samples

Download data: TXT

(Submitter supplied) The discovery, characterization, and adaptation of the RNA-guided clustered regularly interspersed short palindromic repeat (CRISPR)-Cas9 system has greatly increased the ease with which genome and epigenome editing can be performed. Fusion of chromatin-modifying domains to the nuclease-deactivated form of Cas9 (dCas9) has enabled targeted gene activation or repression in both cultured cells and in vivo in animal models. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

11 Samples

Download data: TXT