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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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			Action	DRS
	SRR5052490.fastq.gz	Fastqsanger.gz
	SRR5052500.fastq.gz	Fastqsanger.gz
	SRR5052510.fastq.gz	Fastqsanger.gz
	SRR5052520.fastq.gz	Fastqsanger.gz
	SRR5052530.fastq.gz	Fastqsanger.gz

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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.

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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.

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Project description:Genetic screens help infer gene function in mammalian cells, but it has remained difficult to assay complex phenotypes-such as transcriptional profiles-at scale. Here, we develop Perturb-seq, combining single-cell RNA sequencing (RNA-seq) and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool. We demonstrate Perturb-seq by analyzing 200,000 cells in immune cells and cell lines, focusing on transcription factors regulating the response of dendritic cells to lipopolysaccharide (LPS). Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions. We posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation. By decomposing many high content measurements into the effects of perturbations, their interactions, and diverse cell metadata, Perturb-seq dramatically increases the scope of pooled genomic assays.

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