|
| Status |
Public on Sep 27, 2016 |
| Title |
R6h_infected |
| Sample type |
SRA |
| |
|
| Source name |
from resistant rice variety
|
| Organism |
Ustilaginoidea virens |
| Characteristics |
strain: P1
growth substrate: Inoculated rice panicles
|
| Treatment protocol |
Rice panicles were inoculated with a mixture of conidial and hyphal fragments.
|
| Growth protocol |
The U. virens isolates were cultured in potato sucrose broth (PSB, fresh potato extract and 2 % sucrose) on an incubator shaker at 120 rpm and 28 °C for a week. The panicles of rice plants at the booting stage were inoculated with conidial suspensions (2 × 105 conidia ml−1) at 5 to 7 days before earing.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The pathogen-inoculated panicles were harvested at 6 hpi, 24 hpi and 48 hpi, immediately frozen in liquid nitrogen, and then kept at -70 °C for RNA isolation.
RNA-Seq libraries were constructed following the standard pipeline at Beijing Genomics Institute (BGI) in Shenzhen, China.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw image data were transformed into sequence data by base calling.
All sequences were filtered to remove adaptor sequences and low-quality sequences (where the percentage of the low-quality bases with quality value ≤ 5 was greater than 50% in a read)
The quality-trimmed reads were mapped to U. virens genome using SOAP aligner/SOAP2, allowing up to two base mismatches per read.
The RPKM (reads per kb per million reads) was calculated to reflect the expression level of U. virens transcripts
Genome_build: JHTR00000000
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
Sep 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Wenxian Sun |
| Organization name |
China Agricultural University
|
| Street address |
2 West Yuanmingyuan Rd., Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL22479 |
| Series (1) |
| GSE87345 |
Differential expression profiling of Ustilaginoidea virens in resistant and susceptible rice varieties during early infection |
|
| Relations |
| BioSample |
SAMN05824289 |
| SRA |
SRX2191339 |
