|
| Status |
Public on Mar 16, 2020 |
| Title |
I-L4-2 |
| Sample type |
SRA |
| |
|
| Source name |
miR399f overexpressing line L4 infected with Magnaporthe oryzae 48 hpi
|
| Organisms |
Oryza sativa; Pyricularia oryzae |
| Characteristics |
tissue: leaf
rice cultivar: Tainung67 (japonica)
m. oryzae strain: Guy11
|
| Treatment protocol |
Soil-grown plants (3-4 leaf stage) were mock-inoculated or inoculated with M. oryzae spores for 48hours . Inoculation was done by spraying whole rice plants with a M. oryzae spore suspension (10E5 spores/ml; 0.2 ml/plant) by using an aerograph at 2 atmospheres of pressure
|
| Growth protocol |
Rice plants were grown at 28ºC with a 14 h/10 h light/dark cycle. The fungus M. oryzae was grown in Complete Media Agar (CMA, 9 cm plates, containing 30 mg/L chloramfenicol) for 15 days at 28ºC under a 16 h/8 h light/dark photoperiod condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Maxwell 16 LEV Plant RNA Kit (Promega) following manufacturer's instructions.
Indexed libraries prepared from 1ug purified RNA with TruSeq Stranded mRNA Sample Prep Kit (Illumina). Samples pooled; each index-tagged sample present in equimolar amounts (final concentration of pooled samples at 2nm). Pooled samples subjected to cluster generation and sequencing using Illumina Hseq 2500. 2x100 paired-ennd at final concentration of 8pmol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads were checked for quality by using FastQC v0.11.3
Trimming and removal of adapters involved using Trimmomatic v0.33 (minimum quality score 35, minimum length 25).
The obtained reads were mapped against the Oryza sativa reference genome (MSU 7.0) by using STAR (v2.4.0j)
Alignment files were filtered to remove reads with mapping quality (MAPQ) <30. FeatureCounts (v1.4.5-p1)
Statistical analysis of read counts was performed with R, with the HTSFilter package to remove low-expressed genes and the edge R package
Genome_build: MSU 7.0
Supplementary_files_format_and_content: TXT
|
| |
|
| Submission date |
Sep 19, 2019 |
| Last update date |
Mar 16, 2020 |
| Contact name |
Blanca San Segundo |
| E-mail(s) |
blanca.sansegundo@cragenomica.es
|
| Organization name |
Center for Research in Agricultural Genomics (CRAG)
|
| Department |
Plant Responses to Stress
|
| Street address |
Edifici CRAG - Campus UAB
|
| City |
Bellaterra |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
|
| Platform ID |
GPL27492 |
| Series (1) |
| GSE137735 |
Phosphate excess increases susceptibility to pathogen infection in rice |
|
| Relations |
| BioSample |
SAMN12788356 |
| SRA |
SRX6874256 |
