ArticleGenome research2022
Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling.
Article in Genome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 45 citations in OpenAlex.
- Protocol for identifying cellular and molecular signatures from spatial profiling data using micro-tissue analysis.STAR protocols · 2026Article
- Next-generation kidney tissue analysis - spatial omics and digital pathology.Nature reviews. Nephrology · 2026Review
- Modeling development of tertiary lymphoid structures in pulmonary tuberculosis by 3D profiling and trajectory analysis.bioRxiv : the preprint server for biology · 2026Article
- Spatial transcriptomic landscape of invasion patterns in human papillomavirus-associated endocervical adenocarcinoma.Scientific reports · 2026Article
- Multimodal Spatial Transcriptomics Reveals the Developing Human Liver Niche at Single-Cell Resolution.Gastro hep advances · 2026Article
- Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues.Nature communications · 2025Article
- Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor samples.Nature communications · 2025Article
- Spatial transcriptional landscape of human heart failure.European heart journal · 2025Article
- IgG autoantibodies in bullous pemphigoid induce a pathogenic MyD88-dependent pro-inflammatory response in keratinocytes.Nature communications · 2025Article
- Spatial Transcriptomics Advances the Use of Canine Patients in Cancer Research: Analysis of Osteosarcoma-Bearing Pet Dogs Enrolled in a Clinical Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2025Article
- shinyDSP: a Shiny application for interactive analysis and visualization of NanoString GeoMx Whole Transcriptome Atlas data.Bioinformatics (Oxford, England) · 2025Article
- A single-cell spatial chart of the airway wall reveals proinflammatory cellular ecosystems and their interactions in health and asthma.Nature immunology · 2025Article
- Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity.Nature communications · 2025Article
- Spatial transcriptomics of Glomerulo-centric antibody mediated rejection in renal transplants.Clinical immunology (Orlando, Fla.) · 2025Article
- Spatially resolved transcriptomic profiling for glomerular and tubulointerstitial gene expression in C3 glomerulopathy.Clinical kidney journal · 2025Article
- Novel insights into kidney disease: the scRNA-seq and spatial transcriptomics approaches: a literature review.BMC nephrology · 2025Review
- FGFR antagonists restore defective mandibular bone repair in a mouse model of osteochondrodysplasia.Bone research · 2025Article
- Spatial Transcriptomic Analyses of Spermatogenesis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Spatial Transcriptomics: Integrating Morphology and Molecular Mechanisms of Kidney Diseases.The American journal of pathology · 2025Review
- The tumor microenvironment across four dimensions: assessing space and time in cancer biology.Frontiers in immunology · 2025Review
Corrections and comments
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Authors and funding
24 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Emerging spatial profiling technology has enabled high-plex molecular profiling in biological tissues, preserving the spatial and morphological context of gene expression. Here, we describe expanding the chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed in situ hybridization probes targeting the protein-coding genes of the human and mouse transcriptomes, referred to as the human or mouse Whole Transcriptome Atlas (WTA). Human and mouse WTAs were validated in cell lines for concordance with orthogonal gene expression profiling methods in regions ranging from ∼10-500 cells. By benchmarking against bulk RNA-seq and fluorescence in situ hybridization, we show robust transcript detection down to ∼100 transcripts per region. To assess the performance of WTA across tissue and sample types, we applied WTA to biological questions in cancer, molecular pathology, and developmental biology. Spatial profiling with WTA detected expected gene expression differences between tumor and tumor microenvironment, identified disease-specific gene expression heterogeneity in histological structures of the human kidney, and comprehensively mapped transcriptional programs in anatomical substructures of nine organs in the developing mouse embryo. Digital Spatial Profiling technology with the WTA assays provides a flexible method for spatial whole transcriptome profiling applicable to diverse tissue types and biological contexts.
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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.