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| Status |
Public on Dec 25, 2020 |
| Title |
Single-cell transcriptomic analysis of rice root tips [bulk RNA-seq] |
| Organism |
Oryza sativa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
There are two main types of root systems in flowering plants, which are taproot systems in dicot and fibrous root systems in monocot. The cellular and molecular mechanism involved in root development are mainly from the study of dicot model Arabidopsis thaliana. However, mechanisms of root development and their conservation and divergence in monocot, which including the major crops, remain largely elusive. Here we profile the transcriptomes of more than 20,000 single cells in the root tips of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Single-cell analysis coupled with in situ hybridization identify the cell type-specific marker genes and annotate all the clusters. Comparison of single-cell transcriptome and analysis of mark gene expression suggest well-conserved molecular landscape between rice Nip and 93-11. Moreover, our analysis suggests specific functions gene expression patterns for each cell type cluster, including the hormone genes. Comparison to Arabidopsis single-cell RNA-sequencing dataset reveals extensive differences between Arabidopsis and rice cell types, and species-specific features emphasize the importance of directly studying rice root. Our study reveals transcriptome landscape of major cell types of rice root in singe-cell resolution and provides molecular insight of the cell type morphology of cell type evolution in plants.
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| Overall design |
Bulk RNAseq of protoplast from rice root tips
Please note that each processed data file was generated from both replicates and is linked to the corresponding rep.1 sample records.
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| Contributor(s) |
Liu Q, Liang Z, Gu X |
| Citation(s) |
33352304 |
| |
| Submission date |
Feb 27, 2020 |
| Last update date |
Dec 25, 2020 |
| Contact name |
Xiaofeng Gu |
| E-mail(s) |
guxiaofeng@caas.cn
|
| Organization name |
Chinese Academy of Agricultrual Sciences
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| Street address |
Zhongguancun south street
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| City |
Beijing |
| ZIP/Postal code |
100081 |
| Country |
China |
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| Platforms (1) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE146035 |
Single-cell transcriptomic analysis of rice root tips |
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| Relations |
| BioProject |
PRJNA609101 |
| SRA |
SRP250945 |
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