|
| Status |
Public on Jan 27, 2021 |
| Title |
RAMPAGE_IRBB7_Control_2 |
| Sample type |
SRA |
| |
|
| Source name |
IRBB7
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: IRBB7
tissue: leaves
treatment: Young leaves were inoculated with Xanthomonas oryzae pv. oryzae avrXa7 knockout mutant MX53 (avirulent)
input to technology: 5 ug
technology: RAMPAGE
|
| Treatment protocol |
Leaves of 3 weeks old plants were inoculated with Xanthomonas oryzae pathovar oryzae strain PXO86, and inoculated leaves were subjected to total RNA extraction
|
| Growth protocol |
The rice cultivar IRBB7 was grown in growth chamber at 28 C, 12 hr light and dark with relative humidity 75%
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA extraction performed 24h post-innoculations using TRIzol RNA solution according to manufacturers' recommendations
RAMPAGE; after Batut et al., 2013 (PMID: 24510412)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
TSRsetCombined.tab
TSRsetMerged-1.txt
|
| Data processing |
Library strategy: RAMPAGE
RAMPAGE samples were processed from .fastq to coordinate sorted .bam files using the computational workflow listed here (https://github.com/BrendelGroup/AllRice)
TSSs and TSRs were called using TSRchitect (v1.8.9) as part of the GoSTRIPES workflow. TSSs with less than 3 reads were filtered out, and TSSs within 40 bases were clustered into TSRs.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: TSSset*txt: TSRchitect TSS file
Supplementary_files_format_and_content:TSRset*tab: TSRchitect TSR file
|
| |
|
| Submission date |
Jan 26, 2021 |
| Last update date |
Jan 28, 2021 |
| Contact name |
R. Taylor Raborn |
| E-mail(s) |
[email protected]
|
| Organization name |
Arizona State University
|
| Department |
Center for Mechanisms of Evolution
|
| Lab |
Lynch
|
| Street address |
727 E Tyler St
|
| City |
Tempe |
| State/province |
AZ |
| ZIP/Postal code |
85283 |
| Country |
USA |
| |
|
| Platform ID |
GPL21087 |
| Series (1) |
| GSE165583 |
The Xa7 Resistance Gene Guards the Susceptibility Gene SWEET14 of Rice Against Exploitation by Bacterial Blight Pathogen |
|
| Relations |
| BioSample |
SAMN17595069 |
| SRA |
SRX9951449 |
