|
| Status |
Public on Jul 31, 2022 |
| Title |
R19 4S |
| Sample type |
SRA |
| |
|
| Source name |
sample obtained from ungerminated conidia harvested from Penicillium spp. Grown on PDA plates
|
| Organism |
Penicillium expansum |
| Characteristics |
strain: R19
sample source: ungerminated conidia
|
| Treatment protocol |
ungerminated conidia vs ramifying hyphae extracted from apple tissue
|
| Growth protocol |
Penicillium spp. Grown on PDA medium at 25C before harvesting conidia for apple inoculation or for direct RNA extraction. Apple tissue harvested at leading edge of lesion 5 days postinoculation for fungal RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ungerminated conidia extracted using Trizol method by manufacterer (Invitrogen) using a bead mill. Apple tissue was ground with mortar/pestle in LN2 before using CTAB method followed by cleanup using RNA Extraction Kit (Qiagen).
BGISeq-500 library preparation performed by Beijing Genomics Institute (BGI, China)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
Penicillium spp. Fungal sample
|
| Data processing |
FAST-QC v. 0.11.9
Trinity de novo Alignment to reference (MD-8 genome) usegalaxy.org
Salmon transcriptome read counting usegalaxy.org
Assembly: GCA_000769745.1
Supplementary files format and content: gene count data from transcriptome as aligned to reference genome
|
| |
|
| Submission date |
Jul 28, 2022 |
| Last update date |
Jul 31, 2022 |
| Contact name |
Wayne Jurick II |
| E-mail(s) |
wayne.jurick@usda.gov
|
| Organization name |
USDA-ARS
|
| Department |
Food Quality Lab
|
| Street address |
10300 Baltimore Ave
|
| City |
Beltsville |
| State/province |
MD |
| ZIP/Postal code |
20705 |
| Country |
USA |
| |
|
| Platform ID |
GPL32519 |
| Series (1) |
| GSE209987 |
A Tale of Two Molds: Comparative Penicillium spp. transcriptomics reveals conserved pathways, processes, and loci associated with ungerminated conidia and blue mold decay |
|
| Relations |
| BioSample |
SAMN30025540 |
| SRA |
SRX16717029 |
