|
| Status |
Public on Sep 22, 2015 |
| Title |
M23_30 |
| Sample type |
SRA |
| |
|
| Source name |
Rice-treated Xoo for 30 min
|
| Organism |
Xanthomonas oryzae pv. oryzae KACC 10331 |
| Characteristics |
strain: KACC10331
genotype: wild-type
time point: 30 min
|
| Treatment protocol |
The leaves of rice (Oryza sativa L. cv. Milyang 23) were harvested and homogenized in liquid nitrogen with a mortar and pestle. A culture of Xoo was grown to mid-exponential phase (A600 of 0.5), and 1 g of prepared rice leaf extract (RLX) was then added to the culture medium.
|
| Growth protocol |
The bacterium was grown in Nutrient broth (Difco, Detroit, MI, USA) , and maintained at 28°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each subsample of the harvested Xoo cells separately using the RNeasy Plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Rice-treated Xoo for 30 min
|
| Data processing |
CLC Genomics Workbench 4.0 (CLC bio, Aarhus, Denmark) software used for basecalling.
The relative transcript abundance was calculated by counting the number of reads per kilobase per million mapped sequence reads (RPKM)
Genome_build: ASM738v1 [NC_006834.1]
Supplementary_files_format_and_content: RPKM values for each Sample
|
| |
|
| Submission date |
Sep 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Seunghwan Kim |
| E-mail(s) |
[email protected]
|
| Organization name |
National Academy of Agricultural Science
|
| Department |
Genomics Division
|
| Street address |
Nongsaengmyeong-ro
|
| City |
Jeonju |
| ZIP/Postal code |
560-500 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL19216 |
| Series (1) |
| GSE61607 |
Time-resolved genome-wide pathogenic gene expression analysis of the plant pathogen Xanthomonas oryzae pv. oryzae (Xoo) via RNA-Seq |
|
| Relations |
| BioSample |
SAMN03075461 |
| SRA |
SRX707658 |
