|
| Status |
Public on Jun 29, 2011 |
| Title |
rmc low nitrogen 5 |
| Sample type |
RNA |
| |
|
| Source name |
rmc root, 24h 6.5ppm ammonium treatment
|
| Organism |
Solanum lycopersicum |
| Characteristics |
genotype: rmc
treatment: low nitrogen
tissue: root
|
| Treatment protocol |
ammonium and control treatments were injected into discrete soil patches
|
| Growth protocol |
8 week old tomato plants were transplanted into field soil at Durst Farm, Yolo County CA and grown for an additional 5 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
24 hours post-treatment, patch roots were excised, washed, and frozen. RNA was extracted using a modified Qiagen Rneasy extraction kit
|
| Label |
biotin
|
| Label protocol |
RNA samples were prepared for microarray analysis using the MessageAmp Premier RNA Amplification Kit (Ambion, Foster City CA) with 200 ng total RNA as input
|
| |
|
| Hybridization protocol |
Follow Affymetrix suggested standard method; wash and stain protocol: mini_euk2v3-450, with fluidics station 450
|
| Scan protocol |
Genechipscanner 3000 with 7G upgrade, Software: GCOS v1.4
|
| Data processing |
Signal intenisty data were summarized with MAS5.0 algorithm, log2 transformed and processed with JMP genomics 4.0 software. The probelist was filtered for expressed genes based on Affmetrix expression console sofware PMA designation. ANOVA analysis was performed on all expressed genes to identify significantly differential probesets.
|
| |
|
| Submission date |
Jun 28, 2011 |
| Last update date |
Jun 29, 2011 |
| Contact name |
Dan Ruzicka |
| E-mail(s) |
druzicka@danforthcenter.org
|
| Organization name |
Donald Danforth Plant Science Center
|
| Street address |
975 N. Warson Rd.
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platform ID |
GPL4741 |
| Series (1) |
| GSE30270 |
Transcriptomic and metabolic responses of mycorrhizal roots to nitrogen patches under field conditions |
|
