|
| Status |
Public on Feb 11, 2016 |
| Title |
genotype: Moneymaker - pathogen infection: uninfected - rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Moneymaker_uninfected_root
|
| Organism |
Solanum lycopersicum |
| Characteristics |
germplasm name: Moneymaker
pathogen susceptibility: susceptible
organism part: root ('PO:0009005')
development stage: 2 leaf expansion stage ('PO:0001052')
growth media: vermiculite
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NucleospinRNA Plant (Macherey-Nagel)
|
| Label |
biotin
|
| Label protocol |
Affymetrix one-cycle target labeling
|
| |
|
| Hybridization protocol |
Affy-Eukaryotic Target Hybridization
|
| Scan protocol |
Affy-Array Scanning
|
| Description |
roots of greenhouse-grown tomato plant variety Moneymaker (susceptible to Pyranochaeta lycopersici) mock-treated (May still include original submitter created erros/discrepancies)
|
| Data processing |
The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.
|
| |
|
| Submission date |
Feb 11, 2013 |
| Last update date |
Feb 11, 2016 |
| Contact name |
PLEXdb Curator, Sudhansu Dash |
| Organization name |
Iowa State University
|
| Department |
Virtual Reality Application Center
|
| Lab |
PLEXdb
|
| Street address |
1023 Crop Genomes Informatics Lab (Iowa State University)
|
| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50011 |
| Country |
USA |
| |
|
| Platform ID |
GPL4741 |
| Series (1) |
| GSE44230 |
Gene expression in tomato in response to Pyrenochaeta lycopersici infection |
|
