Single-nucleus and spatial transcriptomics reveal the cell populations of intercalary meristems in bamboo(Dataset ID: STDS0000377)

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Summary
Visualization
Data
Analysis results
Sample
Catalog
Dataset information
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How to cite
Dataset information
Summary:
Intercalary meristems (IcMs), specialized developmental drivers of rapid stem elongation in monocots, exhibit distinct spatiotemporal dynamics. However,However, their genetic basis remains poorly understood due to transient activity and cellular heterogeneity. By combining spatially enhanced resolution omics sequencing (Stereo-seq) and single-nucleus RNA sequencing (snRNA-seq), we reconstruct a dynamic transcriptomic continuum from proliferative to elongation states at single-cell resolution. Integrated multiomics analysis, in situ hybridization and ultrastructural imaging identified IcM cell populations as short-columnar cells adjacent to elongating parenchyma, with the IcM1 subpopulations acting as a stem-like niche essential for maintaining proliferative capacity. This study provides valuable multiomics resources to advance our understanding of IcM identify, function and developmental dynamics in bamboo and other Poaceae species.
Overall design:
To minimize genetic and environmental variability, tissues were harvested from three developmental stages along a single culm of young bamboo shoots (~3 m height): initiation of cell division (ID, 39th internode), rapid cell division phase (RD, 25th internode), rapid elongation phase (RE, 15th internode).  For each stage, tissues were collected from 0.5 cm proximal to the nodal region of corresponding internodes from two biologically independent culms grown under standardized environmental conditions. For snRNA-seq analysis, two biological replicates (n=2 culms) per developmental stage were processed. Concurrently, Stereo-seq samples were prepared by immediately embedding fresh tissues from one representative culm per stage in optimal cutting temperature (OCT) compound (Sakura Finetek) followed by flash-freezing at -80°C for cryopreservation.
Technology:
Stereo-seq | snRNA
Platform:
DNBSEQ-T10 | DNBSEQ-T7 | MGISEQ-2000
Species:
Phyllostachys edulis
Tissues:
Shoot
Development stage:
Rapid growth stage
Submission date: 2025-03-18Update date: 2025-03-18
Sample number: 2Section number: 1
DOI: To be continue
Contributors
Hansheng Zhao
Contact: zhaohansheng@icbr.ac.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] Hansheng Zhao. Single-nucleus and spatial transcriptomics reveal the cell populations of intercalary meristems in bamboo[DS/OL]. STOmicsDB, 2025[2025-03-18]. https://db.cngb.org/stomics/datasets/STDS0000377/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    No results.