|
| Status |
Public on Aug 01, 2023 |
| Title |
UVB-T-41 |
| Sample type |
SRA |
| |
|
| Source name |
True Leaf Tissue
|
| Organism |
Brassica napus |
| Characteristics |
tissue: True Leaf Tissue
genotype: RV31
treatment: UV-B
|
| Treatment protocol |
Plants were harvested 4 hours after exposure to one of the folowng treatments: 4 h irradiation with 3 µmol m−2 s−1 UV-B ('UVB-T') or 70 µmol m−2 s−1 white light in the absence of UV-B ('WL-T;' UV-B control); exogenous application of 4 mL 100 µM MeJA ('MJ-T;' MeJA treatment), 4 mL 0.01% ethanol and 0.01% UN65 ('EU-T;' MeJA control) or 4 mL distilled water ('MC-T;' MeJA control); 1h P. xylostella larvae herbivory ('Plut-T').
|
| Growth protocol |
Brassica napus plants were grown under 70 µmol m−2 s −1 white light for 21 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from leaf tissue using TRIzol® Reagent (Life Technologies) following the manufacturer’s instructions with one minor modification: RNA precipitation was carried out overnight at 4 °C using pre-chilled isopropyl alcohol. DNase treatment of RNA was conducted using the DNA-free™ DNA removal kit (Life Technologies)
TruSeq™ RNA Sample Preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to the Brassica 95K Unigene, B. napus genome and Arabidopsis genome using TopHat v 2.1.12
Differential expression analysis was conducted with Cufflinks v 2.2.1
Arabidopsis gene annotations were assigned to the RNA-seq transcripts based on their sequence similarity to the Arabidopsis genome (TAIR10)
Functional analysis of the RNA-seq transcripts was carried out using the online bioinformatics resource, DAVID (the Database for Annotation, Visualization and Integrated Discovery)
Assembly: GCF_000001735.4
|
| |
|
| Submission date |
Jul 26, 2023 |
| Last update date |
Aug 01, 2023 |
| Contact name |
Kirsty Jamie McInnes |
| E-mail(s) |
[email protected]
|
| Organization name |
Newcastle University
|
| Street address |
Kings road, newcastle university, newcastle upon tyne, NE1 7RU
|
| City |
Newcastle Upon Tyne |
| ZIP/Postal code |
NE1 7RU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL25850 |
| Series (1) |
| GSE239314 |
Overexpression of Brassica napus COMT1 in Arabidopsis heightens UV-B-mediated resistance to Plutella xylostella herbivory |
|
| Relations |
| BioSample |
SAMN36717427 |
| SRA |
SRX21165466 |
