|
| Status |
Public on Oct 06, 2020 |
| Title |
F.mosseae-inoculated-Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Wildtype Rice (cv. Loto) root-inoculated with F. mosseae
|
| Organisms |
Oryza sativa; Funneliformis mosseae |
| Characteristics |
tissue: leaf
rice cultivar: Loto (japonica)
f. mosseae strain: FR140
|
| Treatment protocol |
Rice Loto seeds were dehusked, surface-sterilized twice with 5% sodium hypochlorite for 15 min, and washed extensively with sterile water. Seeds were germinated on petri dishes with sterile water for 7 days and then transplanted to 150ml-cones (20.5 cm; 2 plants/cone) containing a mix of 63.3% quartz sand (0.3-0.8 mm), 31.6% soil (turface and vermiculite 2:1), and 5% of granular inoculum of Funneliformis mosseae. No inoculum was added to the substrate for the non-inoculated, control plants.
|
| Growth protocol |
Non-inoculated and F-mosseae-inoculated transplantes seedlings were grown at the greenhouse under a 14h/10h day/night cycle, 28ºC/25ºC and 60% humidity
|
| 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 |
| |
|
| Description |
SCS19
|
| 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 Japonica (IRGSP-1.0) 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: IRGSP-1.0
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
Apr 13, 2020 |
| Last update date |
Oct 06, 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 |
GPL28382 |
| Series (1) |
| GSE148574 |
Systemic induction of phospholipid-based signaling in leaves of arbuscular mycorrhizal rice plants |
|
| Relations |
| BioSample |
SAMN14592085 |
| SRA |
SRX8110944 |
