|
| Status |
Public on Apr 22, 2024 |
| Title |
Boron, infected biol rep 3 |
| 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 |
BoronIN3
B.napus_RawCounts.txt
S.sclerotiorum_RawCounts.txt
|
| 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 |
| E-mail(s) |
mark.belmonte@umanitoba.ca
|
| 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 mRNA profiling reveals the effect of boron as a crop protection tool against Sclerotinia sclerotiorum |
|
| Relations |
| BioSample |
SAMN41008370 |
| SRA |
SRX24302405 |
