|
| Status |
Public on Aug 28, 2021 |
| Title |
Infected Williams rep 2 [WI-2] |
| Sample type |
SRA |
| |
|
| Source name |
7 day old hypocotyls inoculated with Phytophthora sojae
|
| Organisms |
Glycine max; Phytophthora sojae |
| Characteristics |
cultivar: Soybean cultivar Williams
strain: P. sojae strain P6497
treatment/time point: 12 hours post inoculation
|
| Treatment protocol |
Pathogen treated seedlings were inoculated with 3mm diameter ball of mycelia placed in a vertical slit in the hypocotyl. Mock treated seedling were inoculated with a drop of sterile V8 medium in a vertical slit in the hypocotyl. Inoculations were done at 8am and plants were harvested 12 hr later.
|
| Growth protocol |
Soybean seedlings were grown for 7 days in a growth chamber prior to inoculation. Daytime 27ºC 14 hr. Nightime 21ºC 8 hr. 80% humidity. P. sojae mycelia was grown in V8 liquid medium for three days at 25ºC in the dark.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from plant and mycelia tissues using the Concert™ Plant RNA Reagent Kit, Catalog no. 12322-012. Poly(A)+ RNA was obtained using the promega PolyATtract® mRNA Isolation System.
50 nucleotide paired-end sequencing was carried out by Edge BioServ on their Applied Biosystems SOLiD 3 System
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Description |
processed data file: GmaxRNAseqmappedReads.xlsx; PsojaemergedcufflinkOut.xlsx
|
| Data processing |
Read calling was performed on the Applied Biosystems Whole Transcriptome (WT) Analysis Pipeline
Reads were mapped to soybean Glymax 1.0 gene models and P. sojae Physo 1.0 gene models using Cufflinks
Genome_build: soybean Glymax 1.0 gene models and P. sojae Physo 1.0 gene models from the DOE JGI
Supplementary_files_format_and_content: GmaxRNAseqmappedReads.xlsx is an Excel file. It lists the raw and normalized (FKPM) read numbers for each soybean (Glyma 1.0) gene model found in each of the WI and WM samples. Columns are samples and rows are gene models.
Supplementary_files_format_and_content: PsojaemergedcufflinkOut.xlsx is an Excel file. It lists the raw and normalized (FKPM) read numbers for each P. sojae (Physo 1.0) gene model found in each of the WI and PS samples.Columns are samples and rows are gene models.
|
| |
|
| Submission date |
Aug 25, 2021 |
| Last update date |
Aug 28, 2021 |
| Contact name |
Brett Merrick Tyler |
| E-mail(s) |
brett.tyler@oregonstate.edu
|
| Organization name |
Oregon State University
|
| Department |
Center for Quantitative Life Sciences
|
| Lab |
Tyler lab
|
| Street address |
ALS3021, 2750 Campus Way
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97331 |
| Country |
USA |
| |
|
| Platform ID |
GPL30548 |
| Series (1) |
| GSE182773 |
Host and pathogen gene expression during early infection of soybean seedlings by Phytophthora sojae, analyzed by ABI Solid RNA sequencing |
|
| Relations |
| BioSample |
SAMN20971788 |
| SRA |
SRX11908203 |
