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

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

OTHER RELATED OMICS DATASETS IN: GSE90063

PROVIDER: PRJNA354362 | ENA |

REPOSITORIES: ENA

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

Project description:Methods: We create a CRISPR vector containing a polyadenylated RNA barcode and couple it with droplet scRNA-seq to get a large scale transcriptional measurements of perturbations Results: We were able to perform regulatory inference of gene function, observe nonlinear interactions, and perform downsampling analysis to show that gene signature effects can be seen with as few as 10's of cells while gene level phenotypes, depending on effects size would require 100's of cells Conclusion: Perturb-seq presents a scalable paradigm for obtaining rich genomic profiles of perturbations

2016-12-16 | GSE90063 | GEO

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

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.

| S-EPMC5181115 | biostudies-literature

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

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

| PRJNA354864 | ENA

Compressed Perturb-seq: highly efficient screens for regulatory circuits using random composite perturbations

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.

2023-01-01 | GSE221321 | GEO

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]

2016-12-16 | GSE90486 | GEO

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

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

| PRJNA904326 | ENA

Scalable, compressed phenotypic screening using pooled perturbations (PDAC screens)

Project description:Scalable, compressed phenotypic screening using pooled perturbations (PDAC screens)

| PRJNA1110737 | ENA

Compressed Perturb-seq: highly efficient screens for regulatory circuits using random composite perturbations

Project description:Compressed Perturb-seq: highly efficient screens for regulatory circuits using random composite perturbations

| PRJNA913903 | ENA

Scalable pooled CRISPR screens with single cell chromatin accessibility profiling.

Project description:A scalable, cost-effective method that combines CRISPR perturbations with a single-cell indexing assay for transposase-accessible chromatin (CRISPR-sciATAC). This method links genome-wide chromatin accessibility to genetic perturbations through simultaneous capture of ATAC-seq fragments and CRISPR guide RNAs from single cells using a 96-well plate combinatorial indexing approach.

2020-11-07 | GSE161002 | GEO

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