A spatiotemporal lifecycle atlas decodes spatial coordination in rice(Dataset ID: STDS0000421)

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Summary
Visualization
Data
Sample
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Dataset information
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Dataset information
Summary:
This dataset provides a comprehensive spatiotemporal and single-nucleus transcriptomic atlas across the rice (Oryza sativa, ZH11) seed-to-seed life cycle. It integrates Stereo-seq spatial transcriptomes spanning embryogenesis to maturity with an snRNA-seq atlas of major organs, capturing dynamic gene expression patterns, cell-type heterogeneity, rare cell populations and marker genes. The resource supports identification of stage- and tissue-specific expression, reconstruction of developmental trajectories, and exploration of gene regulatory networks at cellular and spatial resolution.
Overall design:
For spatial profiling (Rice-SpaTempo / A00001), fresh tissues were collected at 43 critical developmental time points of the rice seed-to-seed life cycle, embedded, cryo-sectioned and processed by Stereo-seq. Leaf and stamen cross-sections were analyzed with cell boundary-based binning; other tissues used regular square binning. Unsupervised clustering with t-SNE revealed spatial heterogeneity and led to annotation of 160 cell clusters across 86 sections. For single-nucleus profiling (Rice-SingleCell / A00002), 47 fresh samples (≥1 g tissue each) were used for nuclear extraction; after DAPI staining and QC, libraries were prepared with the DNBelab C series single-cell kit and sequenced on DNBSEQ-T7. After quality control, 851,725 valid nuclei were obtained and partitioned into 113 clusters, of which 99 cell states were annotated using marker genes and spatial transcriptomic data. Processed AnnData releases are ZH11_ST.h5ad, ZH11_ST_supp.h5ad (Stereo-seq) and ZH11_SC.h5ad (snRNA-seq).
Technology:
Stereo-seq | snRNA-seq
Platform:
DNBSEQ-T7 | Stereo-seq | DNBelab C
Tissues:
Germinating embryo|Root|Leaf|Axillary bud|Inflorescence|Spikelet|Pistil|Stamen|Seed|Fertilization
Development stage:
seed|germination|seedling|vegetative|reproductive|lifecycle
Submission date: 2026-10-06Update date: 2026-10-06
Sample number: 90Section number: 86
DOI: To be continue
Contributors
Fan Chen; et al.
Contact: yi.jing@genomics.cn
Accessions
No results.
How to cite
  • Cite database of STOmicsDB:
    [1] Xu, Zhicheng et al. "STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization." Nucleic acids research vol. 52,D1 (2024): D1053-D1061. doi: 10.1093/nar/gkad933'
  • Cite visualization dataset:
    [2] Fan Chen. A spatiotemporal lifecycle atlas decodes spatial coordination in rice[DS/OL]. STOmicsDB, 2026[2026-10-06]. https://db.cngb.org/stomics/datasets/STDS0000421/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    Citation: Jing Y, et al. A spatiotemporal lifecycle atlas decodes spatial coordination in rice. Cell. 2026. doi:10.1016/j.cell.2026.09.023