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Peer-reviewedCC BY-NC 4.0Nucleic Acids Research

STRAND: a comprehensive subcellular-resolved spatial transcriptome RNA architecture and navigation database

  • Zhaoxu Wu1,2
  • Yuying Huo1,2,3
  • Wenqian Xu4
  • Xiangyu Li4
  • Tingting Li1,2,5
5 affiliations
  1. 1Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center , Beijing 100191 ,
  2. 2Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University , Beijing 100191 ,
  3. 3Institute of Biotechnology Innovation, Peking University , Beijing 100871 ,
  4. 4School of Software Engineering, Beijing Jiaotong University , Beijing 100044 ,
  5. 5State Key Laboratory of Natural and Biomimetic Drugs, Peking University , Beijing 100191 ,
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Abstract

Subcellular RNA localization serves as a critical regulatory layer governing cellular polarization, local translation, and functional compartmentalization. Recent advances in high-resolution spatial transcriptomics have provided unprecedented opportunities to resolve these intracellular architectures at single-molecule resolution. However, relevant datasets are dispersed across studies and repositories, vary substantially in processing procedures and standards, severely limiting their cross-study reuse. To bridge this gap, we present STRAND (Subcellular-Resolved Spatial Transcriptome RNA Architecture and Navigation Database), a curated data resource and analysis platform for the automated harvesting, quality control, and interpretation of subcellular spatial transcriptomics data. Through an agent-assisted curation pipeline, STRAND has assembled 35 subcellular-resolution datasets from six major platforms, covering 17 tissue types in human and mouse and totalling ∼4.9 billion transcript coordinates. Building upon this standardized data resource, STRAND provides an analytical workflow spanning cell segmentation evaluation, cell-type annotation, RNA localization/colocalization pattern annotation, and subcellular compartment inference. Two case studies demonstrate that STRAND successfully identifies established RNA localization patterns in cultured cell lines and detects drug-induced RNA relocalization in cardiomyocytes. STRAND is openly available at https://strand.phasep.pro.

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Cite

BibTeXRIS
BibTeX
@article{wu2026strand,
  title = {{STRAND: a comprehensive subcellular-resolved spatial transcriptome RNA architecture and navigation database}},
  author = {Zhaoxu Wu and Yuying Huo and Wenqian Xu and Xiangyu Li and Tingting Li},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag1054},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1054/9005085},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - STRAND: a comprehensive subcellular-resolved spatial transcriptome RNA architecture and navigation database
AU  - Zhaoxu Wu
AU  - Yuying Huo
AU  - Wenqian Xu
AU  - Xiangyu Li
AU  - Tingting Li
PY  - 2026
DA  - 2026/10/30
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1054
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1054/9005085
AB  - Subcellular RNA localization serves as a critical regulatory layer governing cellular polarization, local translation, and functional compartmentalization. Recent advances in high-resolution spatial transcriptomics have provided unprecedented opportunities to resolve these intracellular architectures at single-molecule resolution. However, relevant datasets are dispersed across studies and repositories, vary substantially in processing procedures and standards, severely limiting their cross-study reuse. To bridge this gap, we present STRAND (Subcellular-Resolved Spatial Transcriptome RNA Architecture and Navigation Database), a curated data resource and analysis platform for the automated harvesting, quality control, and interpretation of subcellular spatial transcriptomics data. Through an agent-assisted curation pipeline, STRAND has assembled 35 subcellular-resolution datasets from six major platforms, covering 17 tissue types in human and mouse and totalling ∼4.9 billion transcript coordinates. Building upon this standardized data resource, STRAND provides an analytical workflow spanning cell segmentation evaluation, cell-type annotation, RNA localization/colocalization pattern annotation, and subcellular compartment inference. Two case studies demonstrate that STRAND successfully identifies established RNA localization patterns in cultured cell lines and detects drug-induced RNA relocalization in cardiomyocytes. STRAND is openly available at https://strand.phasep.pro.
SN  - 0305-1048
SN  - 1362-4962
ER  -