ArticleNature communications2023
Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- A multi-modal profiling workflow of transcriptomics and biomineralization demonstrated on a tooth-on-chip model.MethodsX · 2026Article
- RNA-aware tissue preservation workflows for high-quality spatial transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Multi-omics technologies: Novel tools and methods for assessing nerve injury and regeneration.Neural regeneration research · 2026Article
- DeepPathway: predicting pathway expression from histopathology images.Bioinformatics (Oxford, England) · 2026Article
- Human growth plates house resting zone sub-populations with features of quiescent stem cells.Bone research · 2026Article
- Diffusion-based representation integration for foundation models improves spatial transcriptomics analysis.Bioinformatics (Oxford, England) · 2026Article
- Potential of Clinical Care-Collected Gut Biopsies for Advancing Personalised Medicine in Inflammatory Bowel Disease.United European gastroenterology journal · 2026Review
- A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Diffusion-based Representation Integration for Foundation Models Improves Spatial Transcriptomics Analysis.bioRxiv : the preprint server for biology · 2026Article
- Advances in Spatial Transcriptomics in Bone.Current osteoporosis reports · 2026Review
- Spatial AI in cancer: mapping immune evasion topology through multi-modal omics and deep learning.Frontiers in oncology · 2026Review
- Spatial mapping of Ethiopian cutaneous leishmaniasis lesions reveals distinct tissue level immune programs.Frontiers in immunology · 2026Article
- ST-FFPE-mIF: integrating spatial transcriptomics and multiplex immunofluorescence in formalin-fixed paraffin-embedded tissues using Stereo-seq.Genome biology · 2025Article
- Article
- One section, two worlds: single-cell integration of MALDI-MSI and spatial transcriptomics on the same single tissue section.Scientific reports · 2025Article
- Spatial single-cell atlas reveals regional variations in healthy and diseased human lung.Nature communications · 2025Article
- Multi-Modal Foundation Models for Computational Pathology: A Survey.Transactions on machine learning research · 2025Article
- Enhanced RNA Preservation in Mouse Brain Tissue: A Strategy Combining Cardiac Perfusion with Hypersaline Immersion.ACS omega · 2025Article
- Multi-omics approach reveals TGF-β signaling-driven senescence in periodontium stem cells.Journal of advanced research · 2025Article
- Primary cilia in growth plates orchestrate long bone development.Fundamental research · 2025Article
Corrections and comments
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Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of methods targeting the polyA tails of mRNA relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available spatial resolved transcriptomics assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), a workflow designed to improve mRNA recovery from fresh frozen specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we test the RRST protocol on tissue sections collected from five challenging tissue types, including human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyze 52 tissue sections and demonstrate that RRST is a versatile, powerful, and reproducible protocol for fresh frozen specimens of different qualities and origins.
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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.