ASRSSTA: Arabidopsis Shoot Regeneration Single-cell Spatiotemporal Transcriptomic Atlas(Dataset ID: STDS0000237)
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Summary:
Transitions between root and shoot identities are central to plant development and regeneration. Here, we identify a transitional cell (TC) state in Arabidopsis thaliana that bridges these identity switches during de novo shoot regeneration, with parallels suggested during embryogenesis. This TC state consists of two distinct populations: a shoot progenitor population and surrounding boundary cells that collaborate to form a functional shoot system. During a brief transitional phase, these cells exhibit overlapping root- and shoot-specific gene expression, orchestrated by antagonistic interactions between the homeotic factors ATML1 and WOX5. MYB31 is identified as a key regulator that shifts this balance toward shoot formation. By integrating single-nucleus RNA sequencing and spatial transcriptomics, we delineate the molecular signatures, spatial organization, and developmental trajectories of these populations. This study provides a conceptual framework for understanding root-to-shoot transitions and lays the groundwork for engineering plant regeneration, with applications in crop improvement and sustainable agriculture.Overall design:
ASRSSTA database contains the following dataset: 1) bulk RNA-seq data, containing 10 time points from SIM 0 to SIM 18, covered the whole process of shoot regeneration; 2) snRNA-seq data, covering 6 time points from SIM 4 to SIM 16, contained 79,139 single-nucleus transcriptomes from root-drived callus; 3) Stereo-seq data, covering a total of 14 callus tissue sections with 8 sections in SIM 6, 4 sections in SIM 8 and 2 sections in SIM 10.Technology:
Stereo-Seq, scRNA, RNA-seq
Platform:
DNBSEQ-T10
Species:
Arabidopsis thaliana
Tissues:
Callus
Submission date: 2024-02-05Update date: 2024-03-08
Sample number: 61Section number: 14
Contributors
qinchao
Contact: qinchao@genomics.cn
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