ArticleNature biotechnology2020
In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription.
Article in Nature biotechnology, 2020. 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 63 papers.
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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.
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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
63 citing papers in PubMed, 99 citations in OpenAlex.
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- BASELINE: a CRISPR base editing platform for mammalian-scale single-cell lineage tracing.Nucleic acids research · 2026Article
- Lineage tracing from cellular heritage to disease destiny.Nature genetics · 2026Review
- Gigabase-scale deletion scanning of the human genome.bioRxiv : the preprint server for biology · 2026Article
- Spatial instruction of tissue immunity.ImmunoHorizons · 2026Review
- Genetic recording and in situ readout of single-cell signaling memory.Nature chemical biology · 2026Article
- SpaceBar enables single-cell-resolution clone tracing with imaging-based spatial transcriptomics.Nature methods · 2026Article
- Integrated in vivo combinatorial functional genomics and spatial transcriptomics of tumours to decode genotype-to-phenotype relationships.Nature biomedical engineering · 2026Article
- Spatial genomics of AAV vectors reveals mechanism of transcriptional crosstalk that enables targeted delivery of large genetic cargo.Nature biotechnology · 2026Article
- All-optical visualization of specific molecules in the ultrastructural context of brain tissue.Nature biotechnology · 2025Article
- High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer.Science (New York, N.Y.) · 2025Article
- MitoScribe single-cell molecular recorder logs graded signaling dynamics into mitochondrial DNA.bioRxiv : the preprint server for biology · 2025Article
- NIS-Seq enables cell-type-agnostic optical perturbation screening.Nature biotechnology · 2025Article
- High-content image-based pooled screens reveal regulators of synaptogenesis.Cell reports · 2025Article
- Mitochondrial clone tracing within spatially intact human tissues.bioRxiv : the preprint server for biology · 2025Article
- CROPseq-multi: a universal solution for multiplexed perturbation in high-content pooled CRISPR screens.bioRxiv : the preprint server for biology · 2025Article
- Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView.Nature biotechnology · 2025Article
- Advances in optical pooled screening to map spatial complexity.Nature biotechnology · 2025Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Molecular barcoding technologies that uniquely identify single cells are hampered by limitations in barcode measurement. Readout by sequencing does not preserve the spatial organization of cells in tissues, whereas imaging methods preserve spatial structure but are less sensitive to barcode sequence. Here we introduce a system for image-based readout of short (20-base-pair) DNA barcodes. In this system, called Zombie, phage RNA polymerases transcribe engineered barcodes in fixed cells. The resulting RNA is subsequently detected by fluorescent in situ hybridization. Using competing match and mismatch probes, Zombie can accurately discriminate single-nucleotide differences in the barcodes. This method allows in situ readout of dense combinatorial barcode libraries and single-base mutations produced by CRISPR base editors without requiring barcode expression in live cells. Zombie functions across diverse contexts, including cell culture, chick embryos and adult mouse brain tissue. The ability to sensitively read out compact and diverse DNA barcodes by imaging will facilitate a broad range of barcoding and genomic recording strategies.
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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.