|
| Status |
Public on Mar 03, 2020 |
| Title |
33K44_2dpi_2-1 |
| Sample type |
SRA |
| |
|
| Source name |
fungal spores
|
| Organism |
Fusarium verticillioides |
| Characteristics |
inoculum: fungal spores
tissue: infected maize hybrid 33k44 kernels
|
| Treatment protocol |
Fungal spores were inculated directed into maize kernels through sterile needle wounds
|
| Growth protocol |
Maize inbred B73 kernels and maize hybrid 33k44 kernels were inoculated with F. verticillioides wild type and incubated for 2, 4, 6, 8 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each replicate, 10 inoculated kernels were pooled, and total RNA from kernels was extracted.
Standard QA/QC procedure for RNA samples was implemented and library construction was performed at the Texas A&M AgriLife Research Genomics and Bioinformatics Service (College Station, TX).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA sequencing reads were aligned to 'Fusarium verticillioides strain 7600' using TopHat2 and subsequently quantified using HTSeq
Reference genome: Fusarium verticillioides 7600 (Ma et al., 2010)
Since files are paired-end, two corresponding fastq files result in one processed file (i.e., B73_2dpi_1-1_R1.fastq & B73_2dpi_1-1_R2.fastq -> B73_2dpi_1-1.txt)
Supplementary_files_format_and_content: Format is txt and content is read counts
|
| |
|
| Submission date |
Mar 02, 2020 |
| Last update date |
Mar 03, 2020 |
| Contact name |
Man S Kim |
| E-mail(s) |
mandry1979@gmail.com
|
| Organization name |
Texas A&M University
|
| Department |
Plant Pathology & Microbiology
|
| Lab |
Shim Lab.
|
| Street address |
202N LF Peterson, Texas A&M Univ., Plant Pathology & Microbiology
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77840 |
| Country |
USA |
| |
|
| Platform ID |
GPL19800 |
| Series (1) |
| GSE146208 |
Functional subnetwork modules and discovery of hub genes with signal peptide using RNA-Seq (hybrid 33k44 vs. inbred B73) |
|
| Relations |
| BioSample |
SAMN14258370 |
| SRA |
SRX7827055 |
