ArticleScience (New York, N.Y.)2021
In situ genome sequencing resolves DNA sequence and structure in intact biological samples.
Article in Science (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers.
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Who cites it
124 citing papers in PubMed, 206 citations in OpenAlex.
- Spatial chromatin architecture and accessibility co-profiling of mammalian tissues.Nature methods · 2026Article
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Insights Into Spatial Transcriptomics: Exploring Recent Technical Developments and Their Diverse Applications.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Review
- Review
- Single-cell Omics Assessment of Mitochondrial Function: Current Status and Future Perspectives.Genomics, proteomics & bioinformatics · 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
- Machine learning-directed massively parallel programmable nucleic acid amplification.Science advances · 2026Article
- Recurrence plot reconstruction reveals chromosomal reorganization before territory formation.NAR genomics and bioinformatics · 2026Article
- Image-based epigenetic profiling with deep learning and high-speed super-resolution microscopy.Epigenetics & chromatin · 2026Article
- Unified Transcriptome and Mechanics Map of the Intact Mammalian Preimplantation Embryo In Situ.bioRxiv : the preprint server for biology · 2026Article
- Recent advances in methodologies of epigenomics.Epigenomics · 2026Review
- Plants in the expansion era: recent advances in expansion microscopy in plant systems.Journal of experimental botany · 2025Review
- Tracing the evolution of single-cell 3D genomes in Kras-driven cancers.Nature genetics · 2025Article
- Profiling the heterogeneity of microbial populations and communities at the single-cell level.mLife · 2025Review
- Epigenome dynamics in early mammalian embryogenesis.Nature reviews. Genetics · 2025Review
- FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.ArXiv · 2025Article
- Emerging Techniques in Spatial Multiomics: Fundamental Principles and Applications to Dermatology.The Journal of investigative dermatology · 2025Review
- Article
- Single-cell 3D genome reconstruction in the haploid setting using rigidity theory.Journal of mathematical biology · 2025Article
- Quantifying and interpreting biologically meaningful spatial signatures within tumor microenvironments.NPJ precision oncology · 2025Review
64 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors at 5 institutions in 1 country.
Funding
Abstract
Understanding genome organization requires integration of DNA sequence and three-dimensional spatial context; however, existing genome-wide methods lack either base pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across embryonic stages, revealed single-cell chromatin domains in zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how IGS can directly connect sequence and structure across length scales from single base pairs to whole organisms.
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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.