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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: Not available

| S-EPMC5181115 | biostudies-literature

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

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

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

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

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

Mapping and dissecting essential regulatory elements using multi-resolution CRISPR screens

Project description:Hundreds of thousands of candidate cis-regulatory elements (cCREs) have been identified across a myriad of cell types, but relatively few have been empirically characterized. Here, we present a scalable, phenotype-driven CRISPR screening method to test thousands of regulatory elements in parallel, by perturbing thousands of DNase hypersensitive sites (DHS) around hundreds of essential genes in K562. Integrating data from Cas9 exon-targeting with our CRISPRi screens, we nominate and validate promoters that regulate other nearby genes. Using higher-resolution CRISPR systems (dCas9 alone or Cas9) to tile across several essential enhancers, we resolve distinct peaks of activity and dissect core transcription factor binding sites (TFBSs) within enhancers, highlighting the advantages of complementary CRISPR systems to investigate CREs. Lastly, we use our tiling results to interrogate how TFBSs interact to drive enhancer function at the CBFA2T3 locus. This study demonstrates a scalable CRISPR screening framework for identifying and dissecting CREs that regulate cellular phenotypes.

2023-01-31 | GSE216577 | GEO

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