ArticleNature protocols2018
Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections.
Article in Nature protocols, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers.
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Who cites it
123 citing papers in PubMed.
- Integrated single-cell multiomics reveals neutrophil-driven immune-metabolic reprogramming of Kupffer cells via thrombospondin-1/CD36 after surgical stress.JCI insight · 2026Article
- Amplification bias in sequencing-based spatial transcriptomics: sources, mechanisms, impacts, and mitigation strategies.Briefings in bioinformatics · 2026Review
- Spatial and single-nuclei transcriptomics reveals idiosyncratic and generic patterns in papillary and anaplastic thyroid cancers.Molecular oncology · 2026Article
- Article
- Spatial Transcriptomic Atlas Reveals That Forkhead Box O3-Mediated Mitochondrial Dynamics Imbalance Drives Premature Ovarian Insufficiency in Mice.Aging cell · 2026Article
- Spatial transcriptome analysis of the tea tender shoot sheds light on transcriptional regulation of characteristic metabolites.Horticulture research · 2026Article
- Single-Cell Multi-Omics Profiling of Human Septal Myectomy Tissue: Toward Precision Medicine in Obstructive Hypertrophic Cardiomyopathy.Journal of personalized medicine · 2026Review
- Spatiotemporal transcriptomic mapping reveals region-specific glial activation and astrocyte shifts in epileptogenesis beyond the hippocampus.Acta neuropathologica communications · 2026Article
- 3D reconstruction of spatial transcriptomics with spatial pattern enhanced graph convolutional neural network.bioRxiv : the preprint server for biology · 2026Article
- 3D reconstruction of spatial transcriptomics with spatial pattern enhanced graph convolutional neural network.Briefings in bioinformatics · 2026Article
- Progress and challenges in exploring the pathogenesis of depressive disorders via RNA sequencing.Frontiers in genetics · 2026Review
- Tumor Development in Ulcerative Colitis: Perspectives From Biomechanical Characteristics.Development, growth & differentiation · 2025Review
- Article
- Biomaterial-mediated Cell Atlas: an insight from single-cell and spatial transcriptomics.Bioactive materials · 2025Review
- Fibroblasts in the tumor microenvironment: heterogeneity and dynamic interactions in tumor progression revealed by spatial transcriptomics.Cellular oncology (Dordrecht, Netherlands) · 2025Review
- Spatiotemporal multi-omics analysis uncovers NAD-dependent immunosuppressive niche triggering early gastric cancer.Signal transduction and targeted therapy · 2025Article
- Single-cell spatial transcriptomics unravels the cellular landscape of abdominal aortic aneurysm.JCI insight · 2025Article
- An Efficient Organoid Cutting Method for Long-Term Culture and High-Throughput Analyses.Tissue engineering and regenerative medicine · 2025Article
- Advancing muscle aging and sarcopenia research through spatial transcriptomics.Osteoporosis and sarcopenia · 2025Review
- SOAPy: a Python package to dissect spatial architecture, dynamics, and communication.Genome biology · 2025Article
63 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Spatial resolution of gene expression enables gene expression events to be pinpointed to a specific location in biological tissue. Spatially resolved gene expression in tissue sections is traditionally analyzed using immunohistochemistry (IHC) or in situ hybridization (ISH). These technologies are invaluable tools for pathologists and molecular biologists; however, their throughput is limited to the analysis of only a few genes at a time. Recent advances in RNA sequencing (RNA-seq) have made it possible to obtain unbiased high-throughput gene expression data in bulk. Spatial Transcriptomics combines the benefits of traditional spatially resolved technologies with the massive throughput of RNA-seq. Here, we present a protocol describing how to apply the Spatial Transcriptomics technology to mammalian tissue. This protocol combines histological staining and spatially resolved RNA-seq data from intact tissue sections. Once suitable tissue-specific conditions have been established, library construction and sequencing can be completed in ~5-6 d. Data processing takes a few hours, with the exact timing dependent on the sequencing depth. Our method requires no special instruments and can be performed in any laboratory with access to a cryostat, microscope and next-generation sequencing.
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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.