The Single-cell Stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves(Dataset ID: STDS0000104)

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Dataset information
Summary:
We present the first in situ single-cell transcriptome profiling in plant, scStereo-seq (single-cell SpaTial Enhanced REsolution Omics-sequencing), which enabled the bona fide single-cell spatial transcriptome of Arabidopsis leaves.
Overall design:
To enable in situ single-cell level transcriptome analysis in plant leaves, we set out to apply Stereo-seq in Arabidopsis. In this study, combining plant cell wall staining with high- resolution spatial transcriptomics using Stereo-seq, we present the first in situ single-cell transcriptome profiling in Arabidopsis leaves. Single-cell Stereo-seq (scStereo-seq) not only enables us to identify the main leaf cell types, but also allows us to distinguish cell sub-types, including upper and lower epidermal cell, palisade mesophyll cell and spongy mesophyll cell. Furthermore, we also show the existence of cell type-specific spatial gene expression gradients from main vein to leaf edge. We reconstructed those gradients to show for the first time the developmental trajectories of specific cell types according to their spatial distribution.
Technology:
Stereo-Seq
Platform:
DNBSEQ-T10
Species:
Arabidopsis thaliana(tair10)
Tissues:
Leaf
Organ parts:
Cauline leaf
Cell types:
Upper epidermal cell,Lower epidermal cell,Palisade mesophyll cell,Spongy mesophyll cell,Guard cell,V
Development stage:
6 weeks
Submission date: 2022-01-14Update date: 2022-01-14
Sample number: 26
DOI: To be continue
Contributors
Keke Xia,Hai-Xi Sun,Jie Li,Jiming Li,Yu Zhao,Lichuan Chen,Chao Qin,Ruiying Chen,Guangyu Liu,Zhiyong
Contact: xiakeke@genomics.cn
Accessions
Project ID: CNP0002618
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] Keke Xia,Hai-Xi Sun,Jie Li,Jiming Li,Yu Zhao,Lichuan Chen,Chao Qin,Ruiying Chen,Guangyu Liu,Zhiyong . The Single-cell Stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves[DS/OL]. STOmicsDB, 2022[2022-01-14]. https://db.cngb.org/stomics/datasets/STDS0000104/. 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: Xia, Keke et al. “The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves.” Developmental cell vol. 57,10 (2022): 1299-1310.e4. doi:10.1016/j.devcel.2022.04.011