|
| Status |
Public on Jan 26, 2025 |
| Title |
Os mock -Fe 2 |
| Sample type |
SRA |
| |
|
| Source name |
shoots
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: shoots
cultivar: Nipponbare
genotype: WT
treatment: mock -Fe
|
| Treatment protocol |
Plants were regularly irrigated with 1/10 Hoagland media adapted for low (20 µM Fe-EDTA, -Fe), sufficient (20 µM Fe-EDTA, suf) and high (200 µM Fe-EDTA, +Fe) iron availability. For pathogen infections, plants were either mock treated or infected with Colletotrichum higgisianum (Arabidopsis) or Magnaporthe oryzae (rice) suspensions at 10^6 or 10^5 spores/mL, respectively.
|
| Growth protocol |
Arabidopsis thaliana ecotype Col0 and Oyrza sativa subsp. japonica cv. nipponbare were used as wild types. Arabidopsis seeds were stratified at 4 ºC for 2 day and rice seeds germinated at 30 ºC for 2 days on dark. Seeds were sown on a 1:1 mixture of inert substrate ( 33% vermiculite + 66% turbe supplemented with 1g/L CaCO3 ) and washed dorsolite (0.6 to 1.2 mm diameter) and cultivated under a 12 h light (22 ºC and 120 µmols m-2 s-1) / 12h dark (18 ºC) cycle with relative humidity of 65% in FitoClima 1200 PLH LED cabinets (Aralab, Rio de Mouro, Portugal).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 18-day-old rosettes was extracted with the Maxwell® RSC Plant RNA kit (Promega, Wisconsin, USA) according to manufacturer’s indications. RNA quality and integrity was checked in gel.
RNA-Seq libraries were prepared and pair-end sequenced (2x150 bp) at Sistemas Genómicos (València, Spain) with standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
replicate 2
|
| Data processing |
RNA-Seq datasets were analysed on Galaxy (https://usegalaxy.org/).
Assembly: Briefly, reads were cleaned from adapters using Trimmomatic and mapped to the Arabidopsis reference genome (TAIR10) or rice reference genome (IRGSP-1.0) with STAR. Read counts were computed with featureCounts and transcriptional changes were calculated according to Likelihood ratio test hypothesis testing (adjusted P ≤ 0.05) in DESeq2.
Supplementary files format and content: Arabidopsis reference genome (TAIR10) and rice reference genome (IRGSP-1.0)
Supplementary files format and content: csv files containing normalised counts obtained with featureCounts.
|
| |
|
| Submission date |
May 01, 2023 |
| Last update date |
Jan 26, 2025 |
| Contact name |
ANTONI GARCIA-MOLINA |
| E-mail(s) |
[email protected]
|
| Phone |
0034 686672735
|
| Organization name |
Centre for Research in Agrigenomics
|
| Department |
Plant Development and Signal Transduction
|
| Lab |
Gene regulatory networks in plant development
|
| Street address |
Campus UAB - CRAG Building
|
| City |
Cerdanyola del Vallès |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
|
| Platform ID |
GPL18525 |
| Series (1) |
| GSE231365 |
Transcriptome comparison of Arabidopsis and rice responses to fungal infection under different Fe availability periods. |
|
| Relations |
| BioSample |
SAMN34474510 |
| SRA |
SRX20153026 |
