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Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq

ABSTRACT: Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq

PROVIDER: PRJNA354864 | ENA |

REPOSITORIES: ENA

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Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq [SET2]

Project description:In multicellular organisms, dedicated regulatory circuits control cell-type diversity and response. The crosstalk and redundancies within these circuits and substantial cellular heterogeneity pose a major research challenge. We present CRISP-seq, an integrated method for massively parallel single-cell RNA-seq and CRISPR pooled screens. We show that profiling the perturbation and transcriptome in the same cell, enables to elucidate, the function of multiple factors and their interactions. In this benchmarking study, we applied this technology to probe regulatory circuits of innate immunity. By sampling tens of thousands of perturbed cells in vitro and in mice, we identified interactions and redundancies between developmental and signaling-dependent factors controlling the commitment toward different cell lineages or the inflammatory and antiviral pathways. CRISP-seq thereby emerges as a broadly applicable, comprehensive, and unbiased approach for elucidating mammalian regulatory circuits.

2016-12-16 | GSE90487 | GEO

Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq [SET1]

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Perturb-seq: Dissecting molecular circuits with scalable single cell RNA profiling of pooled genetic screens

Project description:Perturb-seq: Dissecting molecular circuits with scalable single cell RNA profiling of pooled genetic screens

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Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-12-16 | GSE90488 | GEO

Pooled CRISPR screens in human intestinal organoids [CRISPR screens]

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Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.

Project description: Not available

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PerturbSci-Kinetics: Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens

Project description:Here we described PerturbSci-Kinetics, a novel combinatorial indexing method for capturing three-layer single-cell readout (i.e., nascent transcriptome, whole transcriptome, sgRNA identities) across hundreds of genetic perturbations. Through PerturbSci-Kinetics profiling of pooled CRISPR screens, we were able to decipher the complexity of RNA dynamics (e.g., synthesis, splicing, and degradation) at both global and gene-specific levels. Our technique opens up the possibility to perform genome-wide perturbations across millions of single cells cost-effectively.

2023-08-10 | GSE218566 | GEO

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