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Sample GSM8216062 Query DataSets for GSM8216062
Status Public on Apr 22, 2024
Title Boron, infected biol rep 2
Sample type SRA
Source name Leaf
Organisms Brassica napus; Sclerotinia sclerotiorum
Characteristics tissue: Leaf
cell line: Cultivar - Westar
treatment: Boron, infected
Treatment protocol Plants were treated with 4.5mL of foliar spray treatment per plant. Treatments consisted of distilled water, 40mM boric acid (as a boron source), and 10 ppm boscalid. Treatment remained on the plants for 24 hours prior to incoulation. As inoculant, 4.0mL of S. sclerotiorum ascospore suspension was sprayed onto plants (1x10^6 spores/mL in potato dextrose broth). Plants then went into a humidty chamber to maintain 90-100% humidity for four day sto allow for infection to progress. At this point, leaves were collected and flash frozen in liquid N as samples for RNA extraction.
Growth protocol Canola (B. napus) cultivar Westar was grown to the 30% flowering stage in Sungrow mix #4 supplemented with Osmocote fertilizer (1.5-2g/pot) in pots sized 8.5cm x 8.5cm x 9cm. Plants were grown in greenhouse, long day conditions.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the Qiagen RNEasy Plant Mini Kit with the addition of Qiagen's on-column DNAse treatment. 1µg of RNA was sent to Genome Québec for library construction.
Genome Québec constructed cDNA libraries according to their mRNA stranded library preparation protocol. Paired-end 100bp reads were sequenced (Illumina NovaSeq 6000)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description BoronIN2
Data processing Read quality was determined using FastQC
Reads were aligned using HISAT2 and raw counts were generated using featureCounts
DESeq2 was used to conduct differencial gene expression analysis
Assembly: B.napus genome v5.0 - GenBank assembly accession: GCA_000751015.1 (Chalhoub et al. 2014)
Assembly: S. sclerotiorum genome - RefSeq assembly accession: GCF_000146945.2 (Amselem et al., 2011)
Supplementary files format and content: B.napus_RawCounts.txt - tab delimited txt file including raw counts for each sample aligned to B. napus
Supplementary files format and content: S.sclerotiorum_RawCounts.txt - tab delimited txt file including raw counts for each sample aligned to S. sclerotiorum
Submission date Apr 18, 2024
Last update date Apr 22, 2024
Contact name Mark Belmonte
Organization name University of Manitoba
Street address 50 Sifton Road
City Winnipeg
State/province MB
ZIP/Postal code R3T 2N2
Country Canada
Platform ID GPL34395
Series (1)
GSE264324 Global RNA sequencing reveals the effect of foliar boron application in protection of Brassica napus against Sclerotinia sclerotiorum infection
BioSample SAMN41008371
SRA SRX24302404

Supplementary data files not provided
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Raw data are available in SRA

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