|
| Status |
Public on Sep 18, 2024 |
| Title |
48AHp |
| Sample type |
SRA |
| |
|
| Source name |
monoculture, control, 48h
|
| Organism |
Hyphopichia pseudoburtonii |
| Characteristics |
tissue: eukaryotic
hp strain: Y963
bc strain: --
treatment: monoculture, control, 48h
|
| Treatment protocol |
H. pseudoburtonii was co-cultured with B. cinerea (coculture/treated), and controlas were prepared by growing H. pseudonurtonii in the absence of B. cinerea (monoculture/control)
|
| Growth protocol |
H. pseudoburtonii Y963 and B .cinerea were maintained on WL agar and Malt extract agar respectively. Bothe cultures were grown at 25°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using a modified version of the hot acidic phenol method originally described by Collart and Oliviero
RNA libraries for RNAISeq were prepared using the Ion Total Transcriptome Sequencing Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent S5 |
| |
|
| Data processing |
STAR 2.6.1
Sequencing reads underwent quality and adaptor contamination checks both before and after trimming using FastQC 0.11.9. Trim Galore 0.6.5 was then employed to eliminate low-quality reads (Q <20), polyA reads, ambiguous reads containing N, and those shorter than 20 nt, while Cutadapt 1.7.1 was used to trim adapters from the remaining reads.
Trimmed sequence reads were mapped to a concatenated genome (Hypbu1+B05. 10). Parameters (Mismatch= (--outFilterMismatchNmax 10)
The GeneCounts function from STAR was used to obtain read counts
Assembly: Hypbu1 and B05. 10
Supplementary files format and content: tab-delimited txt file for each timepoint
|
| |
|
| Submission date |
May 20, 2024 |
| Last update date |
Sep 18, 2024 |
| Contact name |
Evelyn Maluleke |
| E-mail(s) |
evem@sun.ac.za
|
| Phone |
+27 76 968 2661
|
| Organization name |
Stellenbosch University
|
| Department |
Viticulture and Oenology
|
| Lab |
Microbiomics
|
| Street address |
Victoria street
|
| City |
Stellenbosch |
| State/province |
Western cape |
| ZIP/Postal code |
7600 |
| Country |
South Africa |
| |
|
| Platform ID |
GPL34489 |
| Series (1) |
| GSE267877 |
Unravelling the transcriptomic dynamics of Hyphopichia pseudoburtonii in co-culture with Botrytis cinerea |
|
| Relations |
| BioSample |
SAMN41458532 |
| SRA |
SRX24610720 |
