The Single-cell Stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves

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

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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, Vascular cell

Development stage:

6 weeks

Submission date: 2022-01-14Update date: 2022-01-14

Sample number: 26

Contributors

Keke Xia; Hai-Xi Sun; Jie Li; Jiming Li; Yu Zhao; Lichuan Chen; Chao Qin; Ruiying Chen; Guangyu Liu; Zhiyong Chen; Ruilian Yin; Bangbang Mu; Xiaojuan Wang; Mengyuan Xu; Xinyue Li; Yixin Qiao; Peisi Yuan; Shijie Hao; Jing Wang; Qing Xie; Jiangshan Xu; Shiping Liu; Yuxiang Li; Ao Chen; Longqi Liu; Ye Yin; Huanming Yang; Jian Wang; Ying Gu; Xun Xu

Contact: xiakeke@genomics.cn

Accessions

Project ID: CNP0002618

Reference way

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