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

PRJNA237453: Sorghum nitrogen stress tolerance

来源: NCBI / GSE54705
提交时间: Feb 05 2014
释放时间: May 01 2014
最后更新时间: May 15 2019

概要: Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having different genetic backgrounds with contrasting low-N tolerance by the RNAseq deep sequencing data. Several genes were found which are common differentially expressed genes between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three sensitive genotypes (CK60, BTx623 and low-NUE bulk).

项目整体设计: RNAseq deep sequencing

GEN 数据集:
GEND000282
测序方法:
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方案
生长方案: The seeds were grown in three inch pots under a 16/8 h photoperiod at 25°C (day) and 18°C (night).
处理方案: No treatment
提取方案: Total RNA was extracted first using NTES buffer (20 mM TRIS pH 8, 10 mM EDTA, 100 mM NaCl and 1% SDS) and followed by Trizol reagent (Invitrogen) using the manufacturer’s instructions.
建库方案: RNA libraries were prepared from 4 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 - Set A (RS-122-2002) according to the manufacturer’s instructions. Libraries were analyzed and measured by gel electrophoresis and NanoDrop 1000 Spectrophotometer to a concentration of 10 nM each. Four indexed libraries were pooled into one lane and clusters generated at 8 pM concentration were sequenced on the Illumina Genome Analyzer IIx (GAIIx; Illumina, Inc., San Diego, CA) using three 36-cycle sequencing kits to read 76 nucleotides of sequence from a single end of each insert, by standard multiplexing v8.3 protocol.
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 Genome Analyzer IIx
链特异性: Unspecific
样本
基本信息:
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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
Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling.
BMC genomics . 2014-03-05 [PMID: 24597475]