ArticleNature methods2020
Targeted Perturb-seq enables genome-scale genetic screens in single cells.
Article in Nature methods, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 154 papers, 1 of them a synthesis that pooled it.
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Who cites it
154 citing papers in PubMed, 1 synthesis or guideline pooled it, 249 citations in OpenAlex.
- The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases.BMC medical genomics · 2022Pooled it
- Testing the Transferability of Perturbational Similarity Maps Across Species, Cell Systems, and Assay Modalities.Neuroinformatics · 2026Article
- CRISPRing through time: How cutting-edge technology is revolutionizing life sciences and medicine.Molecular therapy. Nucleic acids · 2026Review
- Article
- Benchmarking methods for inferring single-cell transcription factor activity using large-scale perturbation sequencing data.Briefings in bioinformatics · 2026Article
- Improving recombinant protein productivity in CHO cells via multi-omics data integration.Bioresources and bioprocessing · 2026Review
- scGPA: an LLM-assisted workflow for directional virtual gene perturbation analysis from single-cell transcriptomes.BMC genomics · 2026Article
- Mapping enhancer-gene regulatory interactions from single-cell data.Nature genetics · 2026Article
- Perturb-seq reveals TCF7 as a transcriptional link between MAPK- and Wnt-driven gene expression.Nucleic acids research · 2026Article
- Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity.Genome biology · 2026Article
- Comparing machine learning methods predicting transcriptome from epigenome with applications to association studies.Genome biology · 2026Article
- Region-Level Design and Analysis of CRISPR Perturbation Screens with FRACTEL.bioRxiv : the preprint server for biology · 2026Article
- A Comprehensive Review on CRISPR-Based Screening and Its Applications.Molecular biotechnology · 2026Review
- Article
- Article
- Targeted single-cell RNA and perturbation sequencing with TAP-seq.Nature protocols · 2026Review
- PerturbPlan: An analytical framework for designing Perturb-seq experiments.bioRxiv : the preprint server for biology · 2026Article
- Enhancer hubs govern chromatin topology and Th17 cell identity.bioRxiv : the preprint server for biology · 2026Article
- Linking rare variants to cell-type function in profound autism with brain transcriptomics and foundation models.Cell genomics · 2026Review
- MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy.Nature structural & molecular biology · 2026Article
94 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 4 institutions in 4 countries.
Funding
Abstract
The transcriptome contains rich information on molecular, cellular and organismal phenotypes. However, experimental and statistical limitations constrain sensitivity and throughput of genetic screening with single-cell transcriptomics readout. To overcome these limitations, we introduce targeted Perturb-seq (TAP-seq), a sensitive, inexpensive and platform-independent method focusing single-cell RNA-seq coverage on genes of interest, thereby increasing the sensitivity and scale of genetic screens by orders of magnitude. TAP-seq permits routine analysis of thousands of CRISPR-mediated perturbations within a single experiment, detects weak effects and lowly expressed genes, and decreases sequencing requirements by up to 50-fold. We apply TAP-seq to generate perturbation-based enhancer-target gene maps for 1,778 enhancers within 2.5% of the human genome. We thereby show that enhancer-target association is jointly determined by three-dimensional contact frequency and epigenetic states, allowing accurate prediction of enhancer targets throughout the genome. In addition, we demonstrate that TAP-seq can identify cell subtypes with only 100 sequencing reads per cell.
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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.