ArticleNature biotechnology2025
Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView.
Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- Article
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- A pooled image-based CRISPR screen identifies EAF1 as abioRxiv : the preprint server for biology · 2026Article
- A one-week automated genome-wide optical pooled screen using OttoSeq.Genome biology · 2026Article
- Comprehensive resistance profiling of chronic myeloid leukaemia associated ABL1 variants against five tyrosine kinase inhibitors using prime editing.Nature biomedical engineering · 2026Article
- Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects.Cell · 2026Article
- Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT.Nature biotechnology · 2026Article
- Brieflow: an integrated computational pipeline for high-throughput analysis of optical pooled screening data.Nature communications · 2026Article
- Progress and new challenges in image-based profiling.Molecular systems biology · 2026Review
- Virtual cell: Current perspectives and future prospects.The Journal of international medical research · 2026Review
- Spatial profiling of gene editing by in situ sequencing in mice and macaques.Nature biomedical engineering · 2026Article
- Prime editor-based high-throughput screening reveals functional synonymous mutations in human cells.Nature biotechnology · 2026Article
- The one-week automated genome-wide optical pooled screen.bioRxiv : the preprint server for biology · 2026Article
- STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.PLoS computational biology · 2026Article
- Spatial perturb-seq: single-cell functional genomics within intact tissue architecture.Nature communications · 2026Article
- Probing neuropsychiatric disorders through in vivo CRISPR screening.Current opinion in genetics & development · 2026Review
- Bridging the variant-to-function gap in type 2 diabetes: advances and challenges.Diabetologia · 2026Review
- An expanded role for single-cell chemical genomics profiling in drug discovery.The Biochemical journal · 2026Review
- Integrated in vivo combinatorial functional genomics and spatial transcriptomics of tumours to decode genotype-to-phenotype relationships.Nature biomedical engineering · 2026Article
- Next-generation T cell immunotherapies engineered with CRISPR base and prime editing: challenges and opportunities.Nature reviews. Clinical oncology · 2025Review
Corrections and comments
- Erratum issued
Authors and funding
39 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Optical pooled screening (OPS) is a scalable method for linking image-based phenotypes with cellular perturbations. However, it has thus far been restricted to relatively low-plex phenotypic readouts in cancer cell lines in culture due to limitations associated with in situ sequencing of perturbation barcodes. Here, we develop PerturbView, an OPS technology that leverages in vitro transcription to amplify barcodes before in situ sequencing, enabling screens with highly multiplexed phenotypic readouts across diverse systems, including primary cells and tissues. We demonstrate PerturbView in induced pluripotent stem cell-derived neurons, primary immune cells and tumor tissue sections from animal models. In a screen of immune signaling pathways in primary bone marrow-derived macrophages, PerturbView uncovered both known and novel regulators of NF-κB signaling. Furthermore, we combine PerturbView with spatial transcriptomics in tissue sections from a mouse xenograft model, paving the way to in situ screens with rich optical and transcriptomic phenotypes. PerturbView broadens the scope of OPS to a wide range of models and applications.
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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.