Gene Expression
Nebulas
Gene Expression Nebulas概要: RNAseq profiling of seeds and 7 time points during germination in rice under aerobic and anerobic conditions, as well as following re-oxygenation.
项目整体设计: Total RNA was extracted from samples collected at each time point in triplicate. The time points were: 0 h (dry seed), 1 h, 3 h, 12 h, 24 h, 2 days, 3 days and 4 days under aerobic (A) and anaerobic (N) conditions, as well as 3‐day‐old seedlings grown under anaerobic conditions that were switched to air for 1 day.
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| 生长方案: | Rice (Oryza sativa ‘Amaroo’) was de‐hulled, surface sterilised and grown in culture medium [0.5 mm 2‐(N‐morpholine)‐ethanesulphonic acid (MES), 0.4 mm CaSO4, pH 6.5) that was bubbled with air or nitrogen gas (N2) (6–7 L min−1). |
| 处理方案: | For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested. |
| 提取方案: | RNA isolation was carried out using the Sigma Spectrum Plant Total RNA kit. |
| 建库方案: | TruSeq Stranded Total RNA with Ribo‐Zero Plant Sample Prep Kits were used to generate the libraries, according to manufacturer’s instructions (Illumina). rRNAs removed, random fragmentation, stranded library |
| 分子类型: | rRNA- RNA |
| 库的片段类型: | SINGLE |
| 库的链类型: | Forward |
| 测序平台: | ILLUMINA |
| 测序仪型号: | Illumina HiSeq 1500 |
| 链特异性: | Specific |
| 数据来源 | GEN样本编号 | GEN数据集编号 | 系列编号 | 项目编号 | 样本编号 | 样本名称 | 生物样本编号 | 样本访问号 | 实验访问号 | 释放时间 | 提交时间 | 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 |
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