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

PRJNA281369: Host transcriptional reprogramming in response to the rice bacterial blight pathogen Xanthomonas oryzae pv.oryzae constitutively expressing the X. oryzae pv. oryzicola TAL2a effector from the high copy vector pKEB31

来源: NCBI / GSE67958
提交时间: Apr 16 2015
释放时间: May 01 2015
最后更新时间: May 15 2019

概要: We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with Xanthomonas oryzae pv. oryzae strain PXO99A heterologously expressing the Tal2a effector, the designer TAL effector dT280 which targets a sequence overlapping the predicted Tal2a binding sequence in UCH, or the Tal11b effector. Results provide insight into the genes differentially regulated in a Tal2a- and dT280-specific manner.

项目整体设计: Examination of mRNA levels in Oryza sativa L. ssp. japonica cv. Nipponbare leaves at 48 hours after inoculation. Each leaf was considered a separate biological replicate.

GEN 数据集:
GEND000298
测序方法:
物种:
组织:
发育阶段:
方案
生长方案: Oryza sativa L. ssp. japonica cv. Nipponbare plants to be inoculated were grown in LC-1 soil mixture (Sungro, Bellevue, WA) in PGC15 growth chambers (Percival Scientific, Perry, IA) in trays approximately 60 cm below a combination of fluorescent and incandescent bulbs providing approximately 1,000 μmoles/m2/s measured at 15 cm, under a cycle of 12 h of light at 28 °C and 12 h of dark at 25 °C.
处理方案: Plants were inoculated at four weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.9 by infiltration using a needleless syringe. A region from the leaf tip to about 5 cm from the tip was completely infiltrated with contiguous spots. Tissue was collected individually from each leaf after 48 hours.
提取方案: RNA was extracted with the Qiagen RNeasy kit and manufacturer's protocol.
建库方案: These libraries were prepped with the Illumina TruSeq RNA Sample Prep v2 kit
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 2000
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
A transcription activator-like effector from Xanthomonas oryzae pv. oryzicola elicits dose-dependent resistance in rice.
Molecular plant pathology . 2016-04-21 [PMID: 26821568]