PRJNA640389: Single-cell RNA-seq data of Arabidopsis root
概要: We report both raw and processed scRNA-seq data that are used to build transcriptomic atlas of Arabidopsis root.
项目整体设计: scRNA-seq of 18 wild-type, 2 scr-4 and 2 shr-2 mutant Arabidopsis root samples. Three wild-type samples are from published data (two from Denyer et al. 2019 [PMID: 30913408] and one from Ryu et al. 2019 [PMID: 30718350]).
| 生长方案: |
Seeds from wildtype Arabidopsis thaliana ecotype Columbia (Col-0), shortroot-2 (Col-0 background), and scarecrow-4 (Landsberg background backcrossed to Col-0 at least 5 times) were surface sterilized with a 50% (v/v) bleach, 0.05% (v/v) Tween-20 solution for 10 minutes and subsequently stratified for 48 hours at 4°C. Seeds were sown at a density of ~150-300 seeds/row on 1X Linsmaier and Skoog (LSP03-1LT, Caisson Labs; pH 5.7), 1% sucrose media covered by 100/ 47 µm mesh. Plates were placed vertically in a Percival chamber programmed to 16h light, 8h dark conditions at 22°C. |
| 处理方案: |
- |
| 提取方案: |
Chromium Single Cell 3ʹ GEM Kit v3 |
| 建库方案: |
Libraries were prepared for sequencing using 10X Genomics protocols. |
| 分子类型: |
poly(A)+ RNA |
| 库的片段类型: |
PAIRED |
| 库的链类型: |
- |
| 测序平台: |
ILLUMINA |
| 测序仪型号: |
Illumina NovaSeq 6000 |
| 链特异性: |
- |
| 数据来源 |
GEN样本编号 |
GEN数据集编号 |
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项目编号 |
样本编号 |
样本名称 |
生物样本编号 |
样本访问号 |
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最后更新时间 |
物种 |
种族 |
族裔 |
年龄 |
年龄单位 |
性别 |
来源名称 |
组织 |
细胞类型 |
细胞亚型 |
细胞系 |
疾病 |
疾病状态 |
发育阶段 |
突变/变异 |
表型 |
Condition Detail |
生长方案 |
处理方案 |
提取方案 |
建库方案 |
分子类型 |
库的片段类型 |
链特异性 |
库的链类型 |
加标(Spike-In) |
测序方法 |
测序平台 |
测序仪型号 |
细胞数 |
测序片段数 |
碱基数 |
平均测序片段长度_1 |
平均测序片段长度_2 |
唯一比对率 |
多重比对率 |
覆盖度 |
Single-cell analysis of cell identity in the Arabidopsis root apical meristem: insights and opportunities.
Journal of experimental botany . 2021-05-21 [PMID:
34018001]