Ontology highlight
ABSTRACT:
PROVIDER: PRJNA954518 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Human cancer cell lines indicated in the file names, with stably overexpressed Cas9 nuclease, were transfected with (C) control sgRNA or (P) TP53-specific sgRNA, (K) KRAS-specific sgRNA or (M) CMYC-specific sgRNA. Each experiment was done by transfection of sgRNA pair - control (C) or causing a NHEJ-mediated knock-out of the target genes (P, K or M). Samples for proteomics were collected 48h post sgRNA transfection without selection, in three biological replicates each (indicated with numbers 1-3). In cell lines with three activated oncogenes, three separate oncogene-targeting transfections were carried out.
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Project description:Analysis of sgRNA sequences in the raw library and at different time points after transfection into S2R+ cells
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Project description:By a robust unbiased ChIP-seq approach, we demonstrated that CRISPR/Cas9 had crRNA-specific off-target binding activities in human genome. However, most of those binding off-targets could not be efficiently cleaved both in vivo and in vitro which suggested the cleavage off-target activity of CRISPR/Cas9 in human genome is very limited. We provided a valuable tool to further investigate the molecular mechanism of CRISPR/Cas9 and to optimize its in vivo targeting sgRNA binding sites were identified with ChipSeq by using GFP antibody (there are 2 replicates for egfa-t1 sgRNA,emx1 sgRNA and control without sgRNA in Hek293T cells, one egfa-t1 sgRNA,emx1 sgRNA and control without sgRNA in HeLaS3 cells)
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Project description:This dataset contains whole-genome RNA sequencing results from rat embryonic striatal neuronal cultures and serves as the basis for characterization of multiplexed CRISPR/dCas9 gene activation of 16 genes induced by dopamine receptor activation. The goal of this experiment was to define the transcriptional response to multiplexed CRISPR-based upregulation of 16 dopamine-induced genes (Tent5b, Junb, Prox1, Nr4a2, Nptx1, Gsx1, Gadd45g, Btg2, Fosb, Nr4a1, Egr4, Fos, Sstr2, Gadd45b, Egr3, & Egr2), together termed "Dopaplex", as compared to a LacZ control sgRNA.
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Project description: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. Comparing with existing methods, our systems display more robust and specific perturbations of gene transcription with minimal off-targets. Allele-specific targeting of enCRISPRa to oncogenic TAL1 super-enhancer modulates TAL1 expression and cancer progression in xenotransplants. Furthermore, multiplexed perturbations of lineage-specific enhancers in an enCRISPRi knock-in mouse establish in vivo evidence for lineage-restricted requirement of developmentally regulated enhancers during hematopoietic lineage specification. Hence, enhanced CRSIPR epigenetic editing provides opportunities for interrogating enhancer function in development and disease.
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Project description: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. Comparing with existing methods, our systems display more robust and specific perturbations of gene transcription with minimal off-targets. Allele-specific targeting of enCRISPRa to oncogenic TAL1 super-enhancer modulates TAL1 expression and cancer progression in xenotransplants. Furthermore, multiplexed perturbations of lineage-specific enhancers in an enCRISPRi knock-in mouse establish in vivo evidence for lineage-restricted requirement of developmentally regulated enhancers during hematopoietic lineage specification. Hence, enhanced CRSIPR epigenetic editing provides opportunities for interrogating enhancer function in development and disease.
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