ArticleNature biotechnology2024
Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing.
Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 2 of them syntheses that pooled it.
What it found
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Who cites it
33 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Enhancing RNA Capture Efficiency in Spatial Transcriptomics: A Review of Innovative Technologies and Strategies.International journal of molecular sciences · 2025Pooled it
- Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective.Briefings in bioinformatics · 2025Pooled it
- A Method for Imputing scRNA-seq Data Based on Mobile Graph Convolutional Generative Adversarial Networks.Biochemical genetics · 2026Article
- 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
- Spatial-EV-seq: Mapping the spatial organisation of extracellular vesicles in tissues.Clinical and translational medicine · 2026Article
- Amplification bias in sequencing-based spatial transcriptomics: sources, mechanisms, impacts, and mitigation strategies.Briefings in bioinformatics · 2026Review
- Multi-Omics Integration Identifies a CDH3-Associated Malignant Epithelial State and Immunosuppressive Niche to Predict Prognosis in Thymic Epithelial Tumors.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Optics-free spatial genomics for mapping mammalian brain aging by IRISeq.Nature neuroscience · 2026Article
- Spatially resolved profiling of extracellular vesicles in tissues with Spatial-EV-seq.Nature biotechnology · 2026Article
- Mapping the spatial landscape of extracellular vesicles in tissues with Spatial-EV-seq.Nature biotechnology · 2026Article
- A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- [Half a century of gene expression analysis : The path to modern spatial transcriptomics in autopsy tissue].Pathologie (Heidelberg, Germany) · 2026Review
- Tumor heterogeneity as a driver of drug resistance and its implications for personalized therapy.Cancer drug resistance (Alhambra, Calif.) · 2026Review
- Molecular tools for decoding multicellular systems: from mechanisms to medicine.National science review · 2025Review
- BS-D275: A novel locus on the chromosome arm 2DS governing branched spike development in wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- High-plex spatial RNA imaging in one round with conventional microscopes using color-intensity barcodes.Nature biotechnology · 2025Article
- Single-cell sequencing technology in renal cancer: insights into tumor biology and clinical application.Biomarker research · 2025Review
- Multi-omics: a bridge connecting genotype and phenotype for epilepsy?Biomarker research · 2025Review
- SOAR elucidates biological insights and empowers drug discovery through spatial transcriptomics.Science advances · 2025Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Spatial transcriptomics technologies with high resolution often lack high sensitivity in mRNA detection. Here we report a dendrimeric DNA coordinate barcoding design for spatial RNA sequencing (Decoder-seq), which offers both high sensitivity and high resolution. Decoder-seq combines dendrimeric nanosubstrates with microfluidic coordinate barcoding to generate spatial arrays with a DNA density approximately ten times higher than previously reported methods while maintaining flexibility in resolution. We show that the high RNA capture efficiency of Decoder-seq improved the detection of lowly expressed olfactory receptor (Olfr) genes in mouse olfactory bulbs and contributed to the discovery of a unique layer enrichment pattern for two Olfr genes. The near-cellular resolution provided by Decoder-seq has enabled the construction of a spatial single-cell atlas of the mouse hippocampus, revealing dendrite-enriched mRNAs in neurons. When applying Decoder-seq to human renal cell carcinomas, we dissected the heterogeneous tumor microenvironment across different cancer subtypes and identified spatial gradient-expressed genes related to epithelial-mesenchymal transition with the potential to predict tumor prognosis and progression.
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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.