ArticleNature biotechnology2020
Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing.
Article in Nature biotechnology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 286 papers.
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Who cites it
286 citing papers in PubMed, 467 citations in OpenAlex.
- scLDM: a conditional diffusion framework for single-cell perturbation prediction.Bioinformatics (Oxford, England) · 2026Article
- CRISPR-Enabled functional genomics in hPSCs-derived neural models for autism spectrum disorder.Metabolic brain disease · 2026Review
- CRISPRing through time: How cutting-edge technology is revolutionizing life sciences and medicine.Molecular therapy. Nucleic acids · 2026Review
- CFM-GP: unified conditional flow matching to learn gene perturbation across cell types.NAR genomics and bioinformatics · 2026Article
- Integrated epigenetic and genetic programming of primary human T cells.Nature biotechnology · 2026Article
- High-Content CRISPR Screening: Methods and Applications.MedComm · 2026Review
- Characterizing and mitigating cross-library PCR chimeras in Perturb-seq using Perturb-Audit.Blood science (Baltimore, Md.) · 2026Article
- Strategies and mechanisms of precision genome engineering: From gene editing to genome writing.iMetaOmics · 2026Review
- Benchmarking methods for inferring single-cell transcription factor activity using large-scale perturbation sequencing data.Briefings in bioinformatics · 2026Article
- CRISPR-Cas9 and precision editing technologies linking functional genomics to clinical translation in genetic diseases.Clinical and translational medicine · 2026Review
- A Functional Atlas of Transcription Factor-Driven Astrocyte States In Vivo.Neuroscience bulletin · 2026Article
- Towards efficient perturbation for the noncoding genome.Nature communications · 2026Article
- Perturb-seq reveals TCF7 as a transcriptional link between MAPK- and Wnt-driven gene expression.Nucleic acids research · 2026Article
- BASELINE: a CRISPR base editing platform for mammalian-scale single-cell lineage tracing.Nucleic acids research · 2026Article
- CellBouncer, a unified toolkit for single-cell demultiplexing and ambient RNA analysis, reveals hominid mitochondrial incompatibilities.Cell genomics · 2026Article
- Unleashing innovative cross-organ fibrosis therapies by harnessing the omics revolution.JCI insight · 2026Review
- Arrayed single-gene perturbations identify drivers of human anterior neural tube closure.eLife · 2026Article
- Linking GWAS risk genes to transcriptional features of major depressive disorder via in vivo Perturb-seq.Nature genetics · 2026Article
- Single-Cell CRISPR: An Efficient Strategy for Decoding Plant Cis-Regulatory Complexity.Plant biotechnology journal · 2026Review
- Structural evolution of the MTCH family of mitochondrial insertases.Science advances · 2026Article
226 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
17 authors at 3 institutions in 1 country.
Funding
Abstract
Single-cell CRISPR screens enable the exploration of mammalian gene function and genetic regulatory networks. However, use of this technology has been limited by reliance on indirect indexing of single-guide RNAs (sgRNAs). Here we present direct-capture Perturb-seq, a versatile screening approach in which expressed sgRNAs are sequenced alongside single-cell transcriptomes. Direct-capture Perturb-seq enables detection of multiple distinct sgRNA sequences from individual cells and thus allows pooled single-cell CRISPR screens to be easily paired with combinatorial perturbation libraries that contain dual-guide expression vectors. We demonstrate the utility of this approach for high-throughput investigations of genetic interactions and, leveraging this ability, dissect epistatic interactions between cholesterol biogenesis and DNA repair. Using direct capture Perturb-seq, we also show that targeting individual genes with multiple sgRNAs per cell improves efficacy of CRISPR interference and activation, facilitating the use of compact, highly active CRISPR libraries for single-cell screens. Last, we show that hybridization-based target enrichment permits sensitive, specific sequencing of informative transcripts from single-cell RNA-seq experiments.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.