Gene Expression Nebulas
基于标准化流程分析的转录图谱综合数据库

Gene Expression Nebulas

多物种转录图谱整合数据库

PRJNA667059: The mRNA expression profiles of the hypocotyl and root in WT and hy5 (thale cress)

来源: NCBI / GSE158939
提交时间: Oct 02 2020
释放时间: Mar 29 2021
最后更新时间: Mar 29 2021

概要: The mRNA expression profiles of the hypocotyl and root in WT and hy5 were analyzed in 24 hour 22degC and 28degC treated condition. The gene expression changes were analyzed and compared within 22degC and 28degC and in different tissue type (hypocotyl vs root).

项目整体设计: Total twentiefour 24h 22degC and 28degC treated Arabidopsis samples were used. These include three replicates of following genotypes; Col-0 and hy5, with two tissue type; hypocotyl and root. Therefore, three replicates of following genotypes, tissue and conditions; Col-0 (hypocotyl-22degC), Col-0 (root-22degC), hy5 (hypocotyl-22degC), hy5 (root-22degC), Col-0 (hypocotyl-28degC), Col-0 (root-28degC), hy5 (hypocotyl-28degC), hy5 (root-28degC).

GEN 数据集:
GEND000323
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方案
生长方案: Total three genotypes; Col-0, hec1hec2 and pifQ plants were used for mRNA sequencing analysis.
处理方案: The seeds were surface sterilized and plated on the MS media without sucrose, cold stratified for three days in dark to induce germination. After three days, seeds were further treated 5 days in 22℃ with white light (25 µmole/s2/m2). After 5 days, seedlings were either treated with 4 hour of continuous white light (25 µmole/s2/m2) in 22 or 28.
提取方案: Total RNA was isolated using sigma plant total RNA kit(Sigma, Cat.# STRN250).
建库方案: 3'Tag-Seq method article was used to generate TagSeq library according to the manufacturer’s instruction. (doi: 10.1111/1755-0998.12529)
测序信息
分子类型: poly(A)+ RNA
库的片段类型: SINGLE
库的链类型: Reverse
测序平台: ILLUMINA
测序仪型号: Illumina NovaSeq 6000
链特异性: Specific
样本
基本信息:
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质量评估:
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
文章
Spatial regulation of thermomorphogenesis by HY5 and PIF4 in Arabidopsis.
Nature communications . 2021-06-16 [PMID: 34135347]