Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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

OTHER RELATED OMICS DATASETS IN: PRJNA354362

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE90063 | GEO | 2016/12/16

SECONDARY ACCESSION(S): PRJNA354362

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

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

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

| PRJNA354362 | 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

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.

2024-03-14 | GSE220974 | GEO

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

Project description:High-throughput phenotypic screens leveraging biochemical perturbations and high-content readouts are poised to advance therapeutic discovery, yet they remain constrained by limitations of scale. To address this, we establish a method of pooling exogenous perturbations followed by computational deconvolution to compress a screen’s required sample, labor, and financial input. We benchmark the approach with a bioactive small molecule library and a high-content imaging readout, demonstrating the feasibility and increased efficiency of compressed experimental designs compared to conventional approaches. To prove generalizability, we apply compressed screening in two different biological discovery campaigns. In the first, we use early-passage pancreatic cancer organoids to map transcriptional responses to alibrary oftumor-microenvironmentrecombinant protein ligands. We uncover reproducible phenotypic shifts induced by specific ligands that are distinct from canonical reference signatures and uniquely correlate with clinical outcome.In the second, we examine the modulatory effects of a known mechanism of action chemical compound library on primary human peripheral blood mononuclear cell immune responses. Through contrastive analyses, we identify molecules that potentiate and/or inhibit cell-type specific transcriptional features, uncover pleiotropic effects for individual compounds across diverse cell types, and realize a systems-level view of drug responses. In sum, our approach empowers phenotypic screens with information-rich readouts to advance drug discovery efforts as well as basic biological inquiry.

2024-05-13 | GSE267243 | GEO

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

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

| PRJNA1110737 | ENA

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

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

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 | GSE90486 | GEO