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| Status |
Public on Jan 09, 2022 |
| Title |
Single-cell RNA sequencing of tobacco Bright Yellow-2 cell line reveals heterogeneity in cell cycle phase |
| Organism |
Nicotiana tabacum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Cell proliferation and division are fundamental processes of plant development and homeostasis. With the feature of high homogeneity, tobacco Bright Yellow-2 (BY-2) cells, a so-called “HeLa” cell line in plants, provide a useful system for study the cell cycle of plants, particularly when in combination with the latest high-throughput single-cell RNA sequencing (scRNA-seq) technology. Here, we generated both scRNA-seq and bulk RNA-seq data from the BY-2 cells and found that the enzymatic hydrolysis during protoplasting was the major factor contributing to cell clustering noise. We introduced the ppScoring concept to filter out confounding cells due to protoplasting and clustered the remaining cells into clusters corresponding to G0-G1, S, and G2-M phases as well as clusters with phase transition arrested or cell cycle exit cells. The clustering results were supported by cell cycle phase specific marker genes and reconstruction of the continuous full cell cycle phases, i.e., from G0-G1 to S to G2-M, based on pseudotime trajectory analysis. The clustering results also identified a set of 896 cell cycle marker genes. This work demonstrated cell cycle-dependent transcriptional heterogeneity of the BY-2 cell population, provided marker genes for study of the cell cycle of plants and new insights into the progression of cell division.
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| Overall design |
Single cell RNA sequencing for more than 12000 cells (total) from tobacco BY-2 cell line with two replicates. Bulk RNA sequencing for pre- or post-protoplasted BY-2 cells with three replicates in each treatment.
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| Contributor(s) |
Yao J, Chen H, Zhu Q, Fan L, Chu Q |
| Citation missing |
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| |
| Submission date |
Jan 06, 2022 |
| Last update date |
Jan 09, 2022 |
| Contact name |
Yao Jie |
| E-mail(s) |
andy-yaoj@zju.edu.cn
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| Phone |
15158110186
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| Organization name |
ZheJiang University
|
| Street address |
浙江大学紫金港校区农学院A
|
| City |
杭州市 |
| State/province |
浙江 |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platforms (1) |
| GPL29390 |
Illumina NovaSeq 6000 (Nicotiana tabacum) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA795047 |
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