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

PRJNA385135: Variation in transcriptional responses to salt stress in rice

来源: NCBI / GSE98455
提交时间: May 02 2017
释放时间: Jan 01 2018
最后更新时间: May 15 2019

概要: The aim of this study is to assess natural variation in transcriptional responses to salt stress in rice. We utilized a diversity panel (RDP1) described in Zhao et al 2011. Eight day old rice seedlings were subjected to a gradual 6 dS·m-1 salt stress for a period of 24h. RNA seqeuncing was performed on shoot tissue using Illumina HiSeq 2500.

项目整体设计: RNA deep sequencing

GEN 数据集:
GEND000254
测序方法:
物种:
组织:
分离条件:
方案
生长方案: Briefly, plants were grown in a controlled environment growth chamber. Seedlings were transplanted into the pots filled with Turface (Profile Products, LLC) and were grown in tap water for two days after transplanting. For the remainder of the experiment the plants were supplemented with half strength Yoshida solution (pH 5.8). Temperatures were maintained at 28 °C and 25 °C in day and night respectively, relative humidity was maintained at 60% in both day and night. Lighting was maintained at 800 μmoles·m−2·s−1 using high pressure sodium lights.
处理方案: Salinity stress (6:1 molar ratio, NaCl:CaCl2) was increased to 6 dS·m-1 gradually in two 3 dS·m-1 intervals over a period of 24h. After 24h of 6 dS·m-1, aerial parts of the seedlings were excised from the roots and frozen immediately in liquid nitrogen.
提取方案: The samples were ground with Tissuelyser II (Invitrogen) and total RNA was isolated with RNAeasy isolation kit (Qiagen) according to manufacturer’s instructions. On-column DNAse treatment was performed to remove genomic DNA contamination (Qiagen).
建库方案: 96 libraries were prepared using TruSeq RNA v2 library preparation reagents. Eighteen samples were sequenced per lane.
测序信息
分子类型: poly(A)+ RNA
库的片段类型: SINGLE
库的链类型: -
测序平台: ILLUMINA
测序仪型号: Illumina HiSeq 2500
链特异性: Unspecific
样本
基本信息:
样本描述:
生物条件:
实验变量:
方案:
测序信息:
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
Network-based feature selection reveals substructures of gene modules responding to salt stress in rice.
Plant direct . 2019-08-12 [PMID: 31417977]
Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa).
BMC genomics . 2020-06-08 [PMID: 32513103]