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Glioblastoma CRISPR Screen

ABSTRACT: This is an in vitro genome-wide CRISPR/cas9 screen in human glioblastoma stem cells, screening for genes essential for survival of these cells. These cells express cas9 and have been transfected with a guide RNA library causing gene knockouts. We will analyse the sequencing data for depletion of guide RNAs.

PROVIDER: EGAS00001001519 | EGA |

REPOSITORIES: EGA

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CRISPR Screening in Glioblastoma

Project description:This is an in vitro genome-wide CRISPR/cas9 screen in human glioblastoma stem cells, screening for genes essential for survival of these cells. These cells express cas9 and have been transfected with a guide RNA library causing gene knockouts. We will analyse the sequencing data for depletion of guide RNAs. In this particular study, we will do RNA sequencing to correlate CRISPR with expression levels in specific cancer cell subpopulations. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2016-03-22 | E-ERAD-448 | biostudies-arrayexpress

EGAS00001001519-sc-20170427 - samples

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EGAS00001001519-sc-20160602 - samples

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GUIDE-Seq analysis of the designed gRNAs (SG1, SG2, SG3, SG4, SG7 and SG8)

Project description:Off-target (OT) analysis of different guide RNAs targeting PKLR gene. GUIDE-Seq analyses were done in HEK293 cells stably expressing Cas9 transfected with gRNA complexes, generated using Alt-R® CRISPR-Cas9 crRNA XT and Alt-R®CRISPR-Cas9 tracrRNA, and transfected with a dsODN tag

2021-04-13 | GSE171935 | GEO

RNA-Guided Human Gene Activation by Cas9/CRISPR-Based Engineered Transcription Factors

Project description:Synthetic transcription factors can be applied in many areas of biotechnology, medicine, and basic research. In contrast to current methods based on engineering new DNA-binding proteins, we show that Cas9 fused to a transcriptional activation domain can be targeted by combinations of guide RNA molecules to induce the expression of endogenous human genes. This simple approach for targeted gene activation circumvents the need for engineering new proteins and will enable widespread synthetic gene regulation. HEK293T cells were transfected with plasmid expressing Cas9-VP64 fusion protein and a guide RNA. As a control, empty guide RNA was transfected. Gene expression was then measured using mRNA-seq, and differential expression calculated using DESeq. All experiments were performed in biological duplicates or triplicates.

2013-07-25 | E-GEOD-47114 | biostudies-arrayexpress

CRISPR screen to identify regulators of neuronal differentiation

Project description:To search for factors regulating neuronal differentiation, we performed a genome-wide loss-of-function CRISPR/Cas9 screen in haploid human ESCs. The regulators were identified by the quantification of depletion of their mutant clones within a pooled loss-of-function library upon neuronal differentiation.

2024-01-12 | E-MTAB-11944 | biostudies-arrayexpress

Determination of Sox10-regulated genes in the oligodendroglial precursor cell line OLN93

Project description:To determine Sox10-regulated genes in the oligodendroglial precursor cell line OLN93, CRISPR/Cas9-mediated genome editing was performed to inactivate Sox10. For CRISPR/Cas9-mediated Sox10 inactivation, two guide sequences (5’-GCTGCGAGCCAGCCCAGGGCC-3’ for clone A and 5’-GTTGCCCAATTCGCCG GGCCC-3’ for clone B) were separately cloned into pX330. Oln93 cells were co-transfected with pEGFP-N1 and the pX330 plasmids that express the respective guide RNA and SpCas9. Transfected GFP-positive cells were enriched by fluorescence activated cell-sorting and seeded at single cell density in 96-well plates. Homogeneously GFP-expressing clones were analysed for loss of Sox10 protein by immunocytochemistry. Clones without Sox10 protein were obtained with both guide RNAs. Sox10 inactivation was confirmed by Sanger sequencing of the Sox10 gene. RNA was isolated from one clone A and one clone B as well as two independent RNA samples of wildtype OLN93 cells and submitted to RNA-seq.

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Nontargeted metabolomics of UGT71 CRISPR knockouts in Poplar

Project description:Non-targeted metabolomic analysis of UGT71L1 CRISPR-Cas9 knockouts in populus tremula x populus alba

2021-10-29 | ST001962 | MetabolomicsWorkbench

CRISPR-Cas9 RBM10 synthetic lethality screen

Project description:Genome-wide CRISPR-Cas9 knockout screen using TKOv1 sgRNA library was performed in isogenic RBM10-proficient and RBM10-deficient HCC827 cells.

2023-03-04 | E-MTAB-12724 | biostudies-arrayexpress

Identification of genes involved in class switch recombination by genome-wide CRISPR/Cas9 knock-out screen

Project description:This screen aims to identify genes involved in class switch recombination (CSR), a process that allows B cells to change the isotype they express from IgM/IgD to IgG, IgA or IgE. For that purpose, the murine B cell line CH12 stably expressing Cas9 was used. This cell line can be induced to undergo CSR from IgM to IgA very efficiently in vitro when cultured with TGF-b, IL-4 and an anti-CD40 antibody. CH12Cas9 cells were transduced with the second-generation mouse Brie (mBrie) retroviral gRNA library (pMX-mBrie) and selected with puromycin for two weeks to allow for the Cas9-mediated generation of knockouts. Cells were then stimulated to undergo CSR for 72h. Those which failed to undergo CSR (which remained IgM+) or that succeed (which became IgA+) were sorted using magnetic beads. Genes, whose loss-of-function affect the efficiency of CSR, were identified by looking at gRNA enrichment in the IgM+ versus IgA+ populations through deep sequencing.

2021-09-18 | GSE184145 | GEO

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