Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination
IDSTT0000049(Source: STOmics DB)
STOmics technology:BGI Stereomics Stereo-Seq
Organism(s):
Data type:Transcriptome or Gene expression, Spatial transcriptomics
Sample scope:Other
Summary:Characterizing cell features of germinating seeds is essential for understanding the complex biological functions of different embryonic cells in regulating seed vigor and seedling establishment. In this study, we performed spatially enhanced resolution omics (Stereo-seq) and single-cell RNA sequencing (scRNA-seq) to capture spatially resolved single-cell transcriptomes of germinating rice embryos. An automated cell-segmentation model was developed based on deep-learning to accommodate the analysis requirements. The spatial transcriptome revealed known and novel cell types of rice embryo, including two new scutellum cell types. The temporal transcriptome revealed the expression dynamics of genes in different types of embryonic cells during the time course of seed germination and the key genes, particularly related to nutrient metabolism and biosynthesis and signaling of phytohormonesand were reprogrammed in a cell-type-specific manner. Our study provides a panoramic spatiotemporal transcriptome of rice embryo and a novel methodology for exploring the roles of different embryonic cells in seed germination.
Contributor(s):Jie Yao, Qinjie Chu, Nianming Shang.
Publication(s):
- Jie Yao, Qinjie Chu, Nianming Shang. Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination.
Submitter:姚洁(Jie Yao),Zhejiang university
Release date:2023-08-17
Updated:2024-06-11
Relations:
Statistics:
- Sample: 14
- Tissue Section: 14
Datasize:2.51GB
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