ArticleNature methods2022
Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing.
Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
What it found
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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
47 citing papers in PubMed, 65 citations in OpenAlex.
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Photolabile oligonucleotides with topological light gradients enable spatially resolved single-cell transcriptomics and epigenomics.Nature biotechnology · 2026Article
- Quantitative imaging of dynamic processes in intestinal organoids.Nature protocols · 2026Review
- Advancing the Deciphering of Host-Microbe Crosstalk with Spatial Omics: A Mini-Review.Current microbiology · 2026Review
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- dbverse scales spatial omics analysis with embedded analytical databases.bioRxiv : the preprint server for biology · 2026Article
- Imaging-Guided Omics Technologies for Resolving Rare Cancer States and Advancing Nanomedicine.Nano letters · 2026Review
- Imaging-Based Spatial Transcriptomics: Data Interpretation Methods and Biomedical Applications.Biology · 2026Review
- Spatially tunable multiomic sequencing using light-driven combinatorial barcoding of molecules in tissues.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Beyond the Cell Atlas: Functional Communities as the Essential Pathologic Units Driving Kidney Disease.Journal of the American Society of Nephrology : JASN · 2026Review
- A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Light-Guided Molecular Patterning for High-Throughput Single-Molecule Mechanical Characterization.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research.Genomics, proteomics & bioinformatics · 2026Review
- Machine learning-directed massively parallel programmable nucleic acid amplification.Science advances · 2026Article
- Multiplexed optical barcoding and sequencing for spatial omics.Scientific reports · 2026Article
- High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow.Genome research · 2025Article
- Pathogenic morphological signatures of perturbations in mitochondrial-related genes revealed by pooled imaging assay.Npj imaging · 2025Article
- Spatial omics strategies for investigating human carotid atherosclerotic disease.Clinical and translational medicine · 2025Review
- High-throughput sequencing: a breakthrough in molecular diagnosis for precision medicine.Functional & integrative genomics · 2025Review
- Spatial Transcriptomics: Integrating Morphology and Molecular Mechanisms of Kidney Diseases.The American journal of pathology · 2025Review
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 3 countries.
Funding
Abstract
We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking of DNA barcodes onto complementary DNAs in situ with a one-step DNA stitching reaction to create pooled, spatially indexed sequencing libraries. This light-directed barcoding enables in situ selection of multiple cell populations in intact fixed tissue samples for full-transcriptome sequencing based on location, morphology or protein stains, without cellular dissociation. Applying Light-Seq to mouse retinal sections, we recovered thousands of differentially enriched transcripts from three cellular layers and discovered biomarkers for a very rare neuronal subtype, dopaminergic amacrine cells, from only four to eight individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next generation sequencing of the same cells, leaving the sample intact for further analysis post-sequencing.
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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.