ArticleNature methods2017
Pooled CRISPR screening with single-cell transcriptome readout.
Article in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 668 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
668 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genetic landscape and functional exploration of kidney cancer predisposition in cross-ancestral populations.Nature communications · 2026Pooled it
- Single-cell Transcriptomics in Autoimmune Diseases: Mechanistic Insights, Cross-disease Convergence, and Translational Challenges in Rheumatoid Arthritis, Systemic Lupus Erythematosus, Type 1 Diabetes, and Multiple Sclerosis.Clinical reviews in allergy & immunology · 2026Review
- Testing the Transferability of Perturbational Similarity Maps Across Species, Cell Systems, and Assay Modalities.Neuroinformatics · 2026Article
- Article
- CRISPR in clinical oncology: translational advances from molecular diagnostics to therapeutics.Nature reviews. Clinical oncology · 2026Review
- CRISPR-Enabled functional genomics in hPSCs-derived neural models for autism spectrum disorder.Metabolic brain disease · 2026Review
- A systematic comparison of single-cell perturbation response prediction models.Science advances · 2026Article
- CRISPRing through time: How cutting-edge technology is revolutionizing life sciences and medicine.Molecular therapy. Nucleic acids · 2026Review
- 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
- CFM-GP: unified conditional flow matching to learn gene perturbation across cell types.NAR genomics and bioinformatics · 2026Article
- Regulation of mRNA poly(A) tail length governs mammalian body plan formation in gastruloids.Nature communications · 2026Article
- scGPA: an LLM-assisted workflow for directional virtual gene perturbation analysis from single-cell transcriptomes.BMC genomics · 2026Article
- Canon enables causal inference of downstream genes in single-cell CRISPR studies via instrumental variable analysis.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells.Nature biotechnology · 2026Article
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes.Cell genomics · 2026Article
- Single cell CRISPR screen identifies antagonism between Nsd1-H3K36me2 and Ezh2-H3K27me3 orchestrates pluripotency transition.Stem cell reports · 2026Article
- Towards efficient perturbation for the noncoding genome.Nature communications · 2026Article
- Single-Cell and Spatial Omics Technologies in Rice Abiotic Stress Biology: A Methodological Review.International journal of molecular sciences · 2026Review
608 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
Abstract
CRISPR-based genetic screens are accelerating biological discovery, but current methods have inherent limitations. Widely used pooled screens are restricted to simple readouts including cell proliferation and sortable marker proteins. Arrayed screens allow for comprehensive molecular readouts such as transcriptome profiling, but at much lower throughput. Here we combine pooled CRISPR screening with single-cell RNA sequencing into a broadly applicable workflow, directly linking guide RNA expression to transcriptome responses in thousands of individual cells. Our method for CRISPR droplet sequencing (CROP-seq) enables pooled CRISPR screens with single-cell transcriptome resolution, which will facilitate high-throughput functional dissection of complex regulatory mechanisms and heterogeneous cell populations.
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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.