ArticleScience advances2021
XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment.
Article in Science advances, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
- Resolving cell-cell interaction networks and their molecular logic in complex tissues.Nature methods · 2026Article
- 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
- Embryo-scale Visual Cell Sorting reveals a conserved transcriptomic signature of nucleolar size linked to proteostasis.bioRxiv : the preprint server for biology · 2026Article
- A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Beyond the Cell Atlas: Functional Communities as the Essential Pathologic Units Driving Kidney Disease.Journal of the American Society of Nephrology : JASN · 2026Review
- Integrating single-nucleus barcoding with spatial transcriptomics via Stamp-seq to reveal immunotherapy response-enhancing functional modules in NSCLC.Cell discovery · 2026Article
- An expanded role for single-cell chemical genomics profiling in drug discovery.The Biochemical journal · 2026Review
- Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications.Cancer cell · 2026Review
- Spatial information matters: are traditional imputation methods effective for spatial transcriptomics data?Briefings in bioinformatics · 2026Article
- Discovering paracrine regulators of cell type composition from spatial transcriptomics using SPER.Bioinformatics advances · 2026Article
- Review
- Spatial Transcriptomics Decodes Breast Cancer Microenvironment Heterogeneity: From Multidimensional Dynamic Profiling to Precision Therapy Blueprint Construction.Biomolecules · 2025Review
- Tumor-associated mesenchymal stem/stromal cells in tumor microenvironment and carcinogenesis.Experimental hematology & oncology · 2025Review
- Application of single-cell sequencing in the study of immune cell infiltration in inflammatory bowel disease and colorectal cancer.World journal of gastrointestinal oncology · 2025Review
- mNSF: multi-sample non-negative spatial factorization.Genome biology · 2025Article
- High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer.Nature genetics · 2025Article
- Advances in spatial transcriptomics and its application in the musculoskeletal system.Bone research · 2025Review
- Emerging Techniques in Spatial Multiomics: Fundamental Principles and Applications to Dermatology.The Journal of investigative dermatology · 2025Review
- Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics.Nature reviews. Molecular cell biology · 2025Review
- Innovative Insights into Single-Cell Technologies and Multi-Omics Integration in Livestock and Poultry.International journal of molecular sciences · 2024Review
1 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
19 authors.
Funding
Abstract
Single-cell RNA sequencing (scRNA-seq) of tissues has revealed remarkable heterogeneity of cell types and states but does not provide information on the spatial organization of cells. To better understand how individual cells function within an anatomical space, we developed XYZeq, a workflow that encodes spatial metadata into scRNA-seq libraries. We used XYZeq to profile mouse tumor models to capture spatially barcoded transcriptomes from tens of thousands of cells. Analyses of these data revealed the spatial distribution of distinct cell types and a cell migration-associated transcriptomic program in tumor-associated mesenchymal stem cells (MSCs). Furthermore, we identify localized expression of tumor suppressor genes by MSCs that vary with proximity to the tumor core. We demonstrate that XYZeq can be used to map the transcriptome and spatial localization of individual cells in situ to reveal how cell composition and cell states can be affected by location within complex pathological tissue.
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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.