ArticleCell genomics2021
Genome-wide spatial expression profiling in formalin-fixed tissues.
Article in Cell genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- Tumor immune microenvironment alterations using induction cetuximab in a phase II trial of deintensified therapy for p16-positive oropharynx cancer.Head & neck · 2023Trial
- Estimation of cell lineages in tumors from spatial transcriptomics data.Nature communications · 2023Trial
- Mitigating Fixation Artifacts in Spatial Transcriptomics: Methodological Insights from Human Brain Tissue.Molecular neurobiology · 2026Article
- Spatial Transcriptomics for Dissecting Cellular and Molecular Heterogeneity in the Aging and Diseased Brain.International journal of molecular sciences · 2026Review
- Diffusion-based representation integration for foundation models improves spatial transcriptomics analysis.Bioinformatics (Oxford, England) · 2026Article
- ProbeST: a custom probe design pipeline for dual host-pathogen Spatial Transcriptomics.BMC genomics · 2026Article
- Imaging-Based Spatial Transcriptomics: Data Interpretation Methods and Biomedical Applications.Biology · 2026Review
- Multimodal characterisation of spontaneous Merkel cell carcinoma in the endangered Caucasian squirrelJournal of veterinary research · 2026Article
- Pan-cancer analysis of spatial transcriptomics reveals heterogeneous tumor spatial microenvironment.Cell reports. Medicine · 2026Article
- Spatial transcriptomics defines IM-crypt as a premalignant niche with bidirectional divergence in early gastric carcinogenesis.Communications biology · 2026Article
- Transcription Factor TCF12-Mediated Maternal Gene Expressions in Mouse Oocyte Are Prerequisites of Successful Fertilisation and Zygotic Genome Activation.Cell proliferation · 2026Article
- Exploring single-cell and multi-omics technologies and their role in unraveling tumor heterogeneity of hepatocellular carcinoma.Journal of liver cancer · 2026Review
- Probing the Feasibility of Single-Cell Fixed RNA Sequencing from FFPE Tissue.International journal of molecular sciences · 2026Article
- Diffusion-based Representation Integration for Foundation Models Improves Spatial Transcriptomics Analysis.bioRxiv : the preprint server for biology · 2026Article
- stGCL: a versatile cross-modality fusion method based on multi-modal graph contrastive learning for spatial transcriptomics.Genome biology · 2026Article
- A tissue multiplexing approach to maximize spatial omics output from pathology specimens.Frontiers in medicine · 2026Article
- Article
- Advancing Intervertebral Disc Biology via Omics: Implications for Nucleus Pulposus Progenitor Cell-Based Regeneration.JOR spine · 2025Review
- Identification of key molecules in micropapillary progression of lung adenocarcinoma: A comprehensive gene expression analysis study using the spatial gene expression solution methodology.Oncology letters · 2025Article
- From Histology to High-Resolution Mapping: The Rise of Spatial Omics in Immunology.European journal of immunology · 2025Review
5 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here, we report a procedure to perform genome-wide spatial analysis of mRNA in FFPE-fixed tissue sections, using well-established, commercially available methods for imaging and spatial barcoding using slides spotted with barcoded oligo(dT) probes to capture the 3' end of mRNA molecules in tissue sections. We applied this method for expression profiling and cell type mapping in coronal sections from the mouse brain to demonstrate the method's capability to delineate anatomical regions from a molecular perspective. We also profiled the spatial composition of transcriptomic signatures in two ovarian carcinosarcoma samples, exemplifying the method's potential to elucidate molecular mechanisms in heterogeneous clinical samples. Finally, we demonstrate the applicability of the assay to characterize human lung and kidney organoids and a human lung biopsy specimen infected with SARS-CoV-2. We anticipate that genome-wide spatial gene expression profiling in FFPE biospecimens will be used for retrospective analysis of biobank samples, which will facilitate longitudinal studies of biological processes and biomarker discovery.
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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.