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CRISPRai Perturb-seq [Series 1]

ABSTRACT: CRISPRai Perturb-seq [Series 1]

PROVIDER: PRJNA912208 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22741833_1.fastq.gz	Fastqsanger.gz
	SRR22741833_2.fastq.gz	Fastqsanger.gz
	SRR22741834_1.fastq.gz	Fastqsanger.gz
	SRR22741834_2.fastq.gz	Fastqsanger.gz
	SRR22741835_1.fastq.gz	Fastqsanger.gz

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CRISPRai Perturb-seq [Series 1]

Project description:We develop a system for bidirectional epigenetic editing (CRISPRai), in which orthogonal activating (CRISPRa) and repressive (CRISPRi) perturbations are applied simultaneously to multiple loci the same cell. We perform Perturb-seq, a method for single-cell RNA-seq paired with CRISPR guide RNA (gRNA) detection, on cells perturbed using CRISPRai for a panel of pairwise combinations of genes in K562 cells.

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Project description:Pooled CRISPR screens with single-cell RNA-seq readout (Perturb-seq) have emerged as a key technique in functional genomics, but are limited in scale by cost and combinatorial complexity. Here, we reimagine Perturb-seq’s design through the lens of algorithms applied to random, low-dimensional observations. We present compressed Perturb-seq, in which we measure multiple perturbations per cell or multiple cells per droplet, and decompress these measurements by leveraging the sparse structure of regulatory circuits. Applying compressed Perturb-seq to 598 genes in the immune response to bacterial lipopolysaccharide, we achieve the same accuracy as conventional Perturb-seq at 4 to 20-fold reduced cost, with greater power to learn genetic interactions. We identify known and novel regulators of immune responses and uncover evolutionarily constrained genes with downstream targets enriched for immune disease heritability, including many missed by existing GWAS or trans-eQTL studies. Our framework enables new scales of interrogation for a foundational method in functional genomics.

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