PRJNA280380: Host transcriptional reprogramming across diverse strains of the rice bacterial leaf streak pathogen Xanthomonas oryzae pv.oryzicola
概要: We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with 10 geographically diverse strains of Xanthomonas oryzae pv. oryzicola, the causal agent of bacterial leaf streak. Results provide insight into the molecular basis of bacterial leaf streak, particularly the role of transcription activator-like effectors in the disease.
项目整体设计: Examination of mRNA levels in Oryza sativa L. ssp. japonica cv. Nipponbare leaves at 48 hours after inoculation with 10 strains of Xanthomonas oryzae pv.oryzicola with three biological replicates for each compared to three replicates of mock inoculated O sativa as the control
| 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 two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaf. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation. |
| 提取方案: |
RNA was extracted using a modified hot Trizol protocol (Huang et al., 2005) followed by treatment with RNase-free DNase I (Life Technologies, Carlsbad, CA), then purified using the RNeasy MinElute Cleanup kit (Qiagen, Valencia, CA). |
| 建库方案: |
These libraries were prepped with the Illumina TruSeq RNA Sample Prep v2 kit. |
| 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 |
| 数据来源 |
GEN样本编号 |
GEN数据集编号 |
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样本名称 |
生物样本编号 |
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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 |
TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors.
Frontiers in plant science . 2015-07-21 [PMID:
26257749]