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An engineered CRISPR/Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells

ABSTRACT: An engineered CRISPR/Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells

PROVIDER: PRJNA612835 | ENA |

REPOSITORIES: ENA

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An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells.

Project description: Not available

| S-EPMC7529102 | biostudies-literature

An engineered CRISPR/Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells

Project description:Tracing the lineage history of cells is key to answering diverse and fundamental questions in biology. Coupling of cell ancestry information with other molecular readouts represents an important goal in the field. Here, we describe the CARLIN (for CRISPR Array Repair LINeage tracing) mouse line and corresponding analysis tools that can be used to simultaneously interrogate the lineage and transcriptomic information of single cells in vivo. This model exploits CRISPR technology to generate up to 44,000 transcribed barcodes in an inducible fashion at any point during development or adulthood, is compatible with sequential barcoding, and is fully genetically defined. We have used CARLIN to identify intrinsic biases in the activity of fetal liver hematopoietic stem cell (HSC) clones and to uncover a previously unappreciated clonal bottleneck in the response of HSCs to injury. CARLIN also allows the unbiased identification of transcriptional signatures associated with HSC activity without cell sorting.

2020-03-17 | GSE146972 | GEO

Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells

Project description:Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells

| PRJNA624288 | ENA

Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells [CART]

Project description:CRISPR-Cas9 genome editing has enabled advanced T cell therapies, but occasional loss of the targeted chromosome remains a safety concern. To investigate whether Cas9-induced chromosome loss is a universal phenomenon and evaluate its clinical significance, we conducted a systematic analysis in primary human T cells. Arrayed and pooled CRISPR screens revealed that chromosome loss was generalizable across the genome and resulted in partial and entire loss of the chromosome, including in pre-clinical chimeric antigen receptor T cells. T cells with chromosome loss persisted for weeks in culture, implying the potential to interfere with clinical use. A modified cell manufacturing process, employed in our first-in-human clinical trial of Cas9-engineered T cells, dramatically reduced chromosome loss while largely preserving genome editing efficacy. Expression of p53 correlated with protection from chromosome loss observed in this protocol, suggesting both a mechanism and strategy for T cell engineering that mitigates this genotoxicity in the clinic.

2023-11-18 | GSE241838 | GEO

Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells [CROPSeq_Data]

2023-11-18 | GSE241882 | GEO

Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells [Pilot_Data]

2023-11-18 | GSE241839 | GEO

Genetically engineered mouse models of sarcoma using CRISPR/Cas9

Project description:Generation and comparison of CRISPR/Cas9 and Cre-mediated genetically engineered mouse models of sarcoma

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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

Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars

Project description:Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars

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RNA-seq of engineered K562 cell line by CRISPR/Cas9 generation of t(7;12)(q36;p13) chromosomal translocation

Project description:We recreated the t(7;12) translocation in K562 cells by CRISPR/Cas9 to understand its effects on haematopoietic cells, which is of relevance to understand how this cytogenetic abnormalities causes and promotes acute leukaemia in infants. Wild-type K562 were edited by electroporation of ribonucleoprotein complexes consisting of Cas9 enzyme and two guide RNAs targeting patient-specific breakpoint loci. K562 electroporated with Cas9 enzyme only were used as control. Edited K562 harbouring the t(7;12) were single-cell cloned to obtain homogeneous populations (hereby referred to as K562-t(7;12)). We performed RNA sequencing analysis of K562-t(7;12) compared to K562 control to uncover transcriptional changes associated with the translocation.

2022-09-06 | E-MTAB-11851 | biostudies-arrayexpress

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