|
| Status |
Public on Jan 24, 2024 |
| Title |
CDC Falcon spikeletes 7 days post inoculation with F. graminearum 3 |
| Sample type |
SRA |
| |
|
| Source name |
wheat spikelet
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: wheat spikelet
genotype: CDC Falcon
treatment: F. graminearum infected
|
| Treatment protocol |
At 50% of anthers extrusion, single floret inoculation was performed with 10 µL of Fg inoculum at a concentration of 5 x 104 macroconidia /mL, and water (control) between the lemma and palea at the midpoint of the spike
|
| Growth protocol |
seeds were sown in 4” pots with a mixture of 50% Sunshine #5 soilless mix (Sungro, Horticulture Canada, Seba Beach, AB, Canada) and 50% soil, plus 6 g of Osmocote slow release fertilizer (14-14-14; Everris NA, Dublin Ohio, United States). Wheat plants were grown in controlled-environment cabinets with 16 h of light at 22°C and 8 h of dark at 15°C. Plant-prod 20-20-20 soluble fertilizer (Master Plant Products Brampton Ontario, Canada) was applied in the water at a rate of 0.75 g/L and 2 g of slow release fertilizer (14-14-14) was added 40 days after planting. At the three-leaf stage, the plants were thinned to one plant per pot.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed from sectioned rachis node and rachilla samples using the Trizol Reagent (Ambion), according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Falcon_INF_3
|
| Data processing |
Illumina Casava1.7 software used for basecalling
reads trimmed using trimmomatic v0.36 for adapter sequences and low-quality reads
trimmed reads mapped to T. aestivum and F. graminearum using hisat2
count data generated using featureCounts
Differential expression analysis performed using DESeq2
Assembly: T. aestivum IWGSC release 56 ,F. graminearum PH-1 (ASM24013v3)
Supplementary files format and content: tab delimited count data sheets
|
| |
|
| Submission date |
May 25, 2023 |
| Last update date |
Jan 24, 2024 |
| Contact name |
Philip Walker |
| Organization name |
Agriculture and Agri-Food Canada
|
| Street address |
303 Main St
|
| City |
Winnipeg |
| State/province |
Manitoba |
| ZIP/Postal code |
R3C 3G7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18862 |
| Series (1) |
| GSE233409 |
Dual RNA-sequencing of Fusarium Head Blight resistance in winter wheat |
|
| Relations |
| BioSample |
SAMN35363535 |
| SRA |
SRX20514617 |
