|
| Status |
Public on Jan 01, 2024 |
| Title |
NIP_0h_1 |
| Sample type |
SRA |
| |
|
| Source name |
NIP_0h_leaves
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
genotype/variation: NIP
treatment/time point: at 0 hour under Xoo pathotype GIV treatment
developmental stage: at the tillering stage
tissue: Leaf
|
| Treatment protocol |
Leaves were inoculated with Xoo pathotype GIV at the tillering stage by the leaf-clipping method. And leaf samples were collected at 0 and 24 hpi from Nipponbare (NIP), ostopbp1c mutant and OsTOPBP1C-overexpressor, respectively.
|
| Growth protocol |
The Japanica rice (Oryza sativa L.) cultivars Nipponbare (NIP), and transgenic palnts ostopbp1c mutant and OsTOPBP1C-overexpressor, were cultivated in the experimental fields in Beijing
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Every sample was pooled with infected leaves collected from 15 plants in one plot to diminish the individual environment differences.Total RNA from the mentioned samples were extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s recommendation.
NEB Next Poly(A) mRNA Magnetic Isolation Module (NEB) kit was used to enrich the poly(A) tailed mRNA molecules from 1 μg total RNA. The mRNA was fragmented into ~200 base pair pieces. The first-strand cDNA was synthesized from the mRNA fragments reverse transcriptase and random hexamer primers, and then the second-strand cDNA was synthesized using DNA polymerase I and RNaseH. The end of the cDNA fragment was subjected to an end repair process that included the addition of a single “A” base, followed by ligation of the adapters. Products were purified and enriched by polymerase chain reaction (PCR) to amplify the library DNA. The final libraries were quantified using KAPA Library Quantification kit (KAPA Biosystems, South Africa) and an Agilent 2100 Bioanalyzer. After quantitative reverse transcription-polymerase chain reaction (RT-qPCR) validation, libraries were subjected to paired-end sequencing with pair end 150-base pair reading length on an Illumina NovaSeq sequencer (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The sequencing quality were assessed with FastQC (v0.11.5) and then low quality data were filtered using Fastp software.
The clean reads were then aligned to the reference rice genome Oryza_sativa.IRGSP-1.0 using using HISAT2 (v2.1.0) with default parameters.The processed reads from each sample were aligned using HISAT2 against the reference genome
The gene expression analyses were performed with featureCounts and StringTie.
DESeq(v1.28.0) was used to analyze the DEGs between samples. Parameters for classifying significantly DEGs are ≥2-fold differences (|log2FC|≥1, FC: the fold change of expressions) in the transcript abundance and p ≤ 0.05.
Genome_build: Oryza_sativa.IRGSP-1.0
Supplementary_files_format_and_content: abundance measurements
|
| |
|
| Submission date |
Nov 28, 2021 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Wenxue Zhai |
| E-mail(s) |
[email protected]
|
| Phone |
010-64807633
|
| Organization name |
Institute of Genetics and Developmental Biology
|
| Department |
Molecular Agrobiology
|
| Lab |
Wenxue Zhai
|
| Street address |
NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL27860 |
| Series (1) |
| GSE189719 |
The interfering transcription activator-like effector DR16 and OsSOG1 attenuates OsTOPBP1C-activated rice bacterial blight resistance |
|
| Relations |
| BioSample |
SAMN23481370 |
| SRA |
SRX13244404 |
