|
| Status |
Public on Mar 24, 2010 |
| Title |
root_lowN_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
wild-type 76R
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: root
strain: 76R
|
| Treatment protocol |
The low N treatment was 6.5ug NH4+-N per gram of soil. Ammonium treatments were injected into discrete soil patches
|
| Growth protocol |
tomato plants transplanted into field soil collected at Durst Farm, Yolo County CA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
53 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, natural log transformed and processed with JMP genomics 3.0 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 |
Mar 23, 2010 |
| Last update date |
Mar 23, 2010 |
| 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) |
| GSE21020 |
Tomato root transcriptome response to a nitrogen-enriched soil patch |
|
