|
| Status |
Public on Nov 07, 2017 |
| Title |
12h.NormalTemp.X115A-avrXa7.1 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf Tissue
|
| Organism |
Oryza sativa Indica Group |
| Characteristics |
tissue: leaf
cultivar: IRBB61
hours post-inoculation: 12 h
temperature: Normal Temperature
pathogen treatment: Xo X11-5A (avrXa7)
|
| Treatment protocol |
Plant leaves were inoculated with dilutions of overnight cultures of Xanthomonas oryzae strain X11-5A carrying pKEB31 plasmids containing ORFs for avrXa7 and talΔCRR (a non-functional TAL effector lacking the DNA binding region), and water. Six infiltration sites were used along a 4 cm section of each leaf.
|
| Growth protocol |
Seeds of rice variety IRBB61 were germinated on wet filter paper under constant light at 28°C. After emergence, the seedlings were transplanted in soil in a greenhouse (approximately 23°/18°C day/night, 75-85% relative humidity) and grown for three weeks. The plants were evenly distributed to two growth chambers set to normal (29°/23°C day/night) and high (35°/29°C day/night) temperature regimes and 85% relative humidity. Plants were acclimated to growth chambers for one week before inoculations.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from plant tissue with Sigma Aldrich Spectrum Plant Total RNA Kit.
Libraries were constructed with Illumina TruSeq RNA Library Prep Kits.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence and low quality sequence using FASTX Toolit 0.0.14.
Reads were aligned to the MSU RGAP 7.0 rice reference genome using TopHat 2.1.1 with BowTie 2.2.9.
Gene counts were generated from the aligned reads with HTSeq 0.6.1.
Genome_build: MSU RGAP 7.0
Supplementary_files_format_and_content: CountsTable.txt.gz is a tab-separated text file that contains gene counts for all samples
|
| |
|
| Submission date |
Mar 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Philip Cohen |
| E-mail(s) |
stephen.cohen@colostate.edu
|
| Organization name |
Colorado State University
|
| Department |
Bioagricultural Sciences and Pest Management
|
| Lab |
Jan Leach Lab
|
| Street address |
1177 Campus Delivery
|
| City |
Fort Collins |
| State/province |
CO |
| ZIP/Postal code |
80523 |
| Country |
USA |
| |
|
| Platform ID |
GPL21027 |
| Series (1) |
| GSE95668 |
Rice plants exhibiting bacterial blight resistance at high temperature suppress abiotic response |
|
| Relations |
| BioSample |
SAMN06473532 |
| SRA |
SRX2611283 |
