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Sample GSM7427140 Query DataSets for GSM7427140
Status Public on Jan 24, 2024
Title water inoculated spikelet in AC Morley 2
Sample type SRA
 
Source name wheat spikelet
Organism Triticum aestivum
Characteristics tissue: wheat spikelet
genotype: AC Morley
treatment: uninfected
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 Morley_CTL_2
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 SAMN35363542
SRA SRX20514610

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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