|
| Status |
Public on Dec 21, 2017 |
| Title |
3 dpi wild type 5 |
| Sample type |
SRA |
| |
|
| Source name |
3 dpi wild type
|
| Organisms |
Zea mays; Fusarium verticillioides |
| Characteristics |
host: maize
maize strain: maize (B73)
tissue: Fungal mycelia and maize stalk mixture
fungal genotype: wildtype
time (dpi): 3
|
| Treatment protocol |
Fungal spores were inculated directed into maize stalks through sterile needle wonds
|
| Growth protocol |
Maize inbred B73 stalks were inoculated with F. verticillioides wild type and fsr1 mutant and incubated for 3, 6, d days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each sample, sectioning was performed on at least three independent stalk samples from each stage of infection, and isolated tissues were pooled for RNA extraction with Trizol reagent (Invitrogen).
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 2000 |
| |
|
| Data processing |
Illumina’s HCS 1.5.15.1 and RTA 1.13.48.0 were used for basic processing such as quality prefiltering, base calling, and uncertainty assessment
RNA sequencing reads were aligned to 'Fusarium verticillioides strain 7600' using Bowtie2
Reads were counted with Samtools
Genome_build: http://fungi.ensembl.org/Fusarium_verticillioides/Info/Index
Supplementary_files_format_and_content: text file with read counts
|
| |
|
| Submission date |
Dec 20, 2017 |
| Last update date |
Jan 23, 2018 |
| 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 |
GPL24415 |
| Series (1) |
| GSE108365 |
Functional subnetwork modules and hub gene discovery using RNA-Seq (wild type Fusarium verticillioides and the FSR1 mutant) |
|
| Relations |
| BioSample |
SAMN08214641 |
| SRA |
SRX3491046 |
