|
| Status |
Public on Jun 18, 2023 |
| Title |
D4 |
| Sample type |
SRA |
| |
|
| Source name |
Botrytis cinerea (strain B05.10)
|
| Organism |
Botrytis cinerea |
| Characteristics |
sample type: High 29C 8h + 37C 2h
|
| Treatment protocol |
Treatments included incubation at 22°C or 29°C for 10 h (OT and MHT, respectively), followed by 22°C or 29°C for 8 h and 37°C for 2 h (SHT and SHT-P, respectively). GTs were collected from the plates by washing with water, centrifuged, separated into two 1.5-ml Eppendorf tubes, flash-frozen in liquid nitrogen and stored at –80°C.
|
| Growth protocol |
B. cinerea strain B05.10 and derived transgenic strains were routinely cultured on potato dextrose agar (PDA, Acumedia) or suspended in potato dextrose broth (PDB) at 22°C under continuous fluorescent light supplemented with near UV light. Additional media that were used for specific experiments included malt medium (5 g glucose, 15 g malt extract, 1 g peptone, 1 g casamino acids) and GB5-Glc medium (Gamborg B5 with vitamins and 2% glucose, Duchefa Biochemie). B. cinerea cultures were produced by spreading 500 μl of spore suspension (107/ml) on a cellophane-covered PDA plate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol reagent (Sigma-Aldrich) according to the manufacturer’s instructions.
cDNA libraries were prepared using a NEBNext Ultra II RNA Library Prep Kit (NEB). RNA and cDNA quality and quantity were evaluated by performing a Qubit assay with the TapeStation 4200 system (Agilent Technologies). Sequencing libraries were constructed with barcodes using NEBNext multiplex oligos for Illumina (NEB).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
D4_S16
|
| Data processing |
Partek® Flow® (build version 9.0.20.0804)
Bases were trimmied on quality score=20. Adaptors were also trimmed.
Filter BAM files with minimal mapping quality=20.
Alignment usign STAR - 2.7.3a to B. cinerea reference genome (assembly ASM14353v4)
Quantification to transcriptome performed using Partek E/M algorithm.
Assembly: B. cinerea reference genome (assembly ASM14353v4)
|
| |
|
| Submission date |
Oct 25, 2022 |
| Last update date |
Jun 18, 2023 |
| Contact name |
Metsada Pasmanik-Chor |
| E-mail(s) |
metsada@tauex.tau.ac.il
|
| Organization name |
Tel Aviv University
|
| Department |
Biology
|
| Lab |
Bioinformatics Unit
|
| Street address |
Ramat Aviv
|
| City |
Tel Aviv |
| ZIP/Postal code |
69978 |
| Country |
Israel |
| |
|
| Platform ID |
GPL24810 |
| Series (1) |
| GSE216541 |
Increased protein solubility contributes to heat priming of the plant pathogenic fungus Botrytis cinerea |
|
| Relations |
| BioSample |
SAMN31440373 |
| SRA |
SRX18016140 |
