|
Status |
Public on Mar 03, 2020 |
Title |
33K44_6dpi_3-2 |
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).
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|
|
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
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|
|
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 |
SAMN14258253 |
SRA |
SRX7827086 |