Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome DOI Creative Commons
Eli Metzner, Kaden M. Southard, Thomas M. Norman

et al.

Cell Systems, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Single-cell CRISPR screens link genetic perturbations to transcriptional states, but high-throughput methods connecting these induced changes their regulatory foundations are limited. Here, we introduce Multiome Perturb-seq, extending single-cell simultaneously measure perturbation-induced in gene expression and chromatin accessibility. We apply Perturb-seq a CRISPRi screen of 13 remodelers human RPE-1 cells, achieving efficient assignment sgRNA identities single nuclei via an improved method for capturing barcode transcripts from nuclear RNA. organize accessibility measurements into coherent programs describing the integrated effects on cell state, finding that ARID1A SUZ12 knockdowns induce enriched developmental features. Modeling heterogeneity connects expression, highlighting value multimodal profiling. Overall, our provides scalable simply implemented system dissect logic underpinning state. A record this paper's transparent peer review process is included supplemental information.

Language: Английский

Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2 DOI Creative Commons
Henri Schmidt, Minsi Zhang,

Dimitar Chakarov

et al.

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 26, 2025

Abstract We present GuideScan2 for memory-efficient, parallelizable construction of high-specificity CRISPR guide RNA (gRNA) databases and user-friendly design analysis individual gRNAs gRNA libraries targeting coding non-coding regions in custom genomes. identifies widespread confounding effects low-specificity published screens enables a library that reduces off-target gene essentiality screen. also the experimental validation allele-specific hybrid mouse genome. will facilitate experiments across wide range applications.

Language: Английский

Citations

0
Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome DOI Creative Commons
Eli Metzner, Kaden M. Southard, Thomas M. Norman

et al.

Cell Systems, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Single-cell CRISPR screens link genetic perturbations to transcriptional states, but high-throughput methods connecting these induced changes their regulatory foundations are limited. Here, we introduce Multiome Perturb-seq, extending single-cell simultaneously measure perturbation-induced in gene expression and chromatin accessibility. We apply Perturb-seq a CRISPRi screen of 13 remodelers human RPE-1 cells, achieving efficient assignment sgRNA identities single nuclei via an improved method for capturing barcode transcripts from nuclear RNA. organize accessibility measurements into coherent programs describing the integrated effects on cell state, finding that ARID1A SUZ12 knockdowns induce enriched developmental features. Modeling heterogeneity connects expression, highlighting value multimodal profiling. Overall, our provides scalable simply implemented system dissect logic underpinning state. A record this paper's transparent peer review process is included supplemental information.

Language: Английский

Citations

2