|
| Status |
Public on Sep 06, 2010 |
| Title |
Iso 10DAP, Fe limited, biological rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
IsoClark 10 day roots, Fe limited, biological rep 3
|
| Organism |
Glycine max |
| Characteristics |
isogenic line: IsoClark
time point: 10 days
condition: Fe limited
biological replicate: 3
tissue: Total Roots
|
| Treatment protocol |
plants were grown in either iron sufficient (100uM Fe(NO3)3) or iron limited (50uM Fe(NO3)3) hydroponic conditions. After 10 days, the roots of half the plants were collected in liquid nitrogen. 12 days after planting, Iron was added to all remaining hydroponic solutions to either bring the iron levels up to iron sufficient conditions or maintain iron sufficient growth conditions. 14 days after planting, the remaining plant roots were harvested in liquid nitrogen.
|
| Growth protocol |
seeds were germinated on germination paper in growth chambers for 1 week. Seedlings were transferred to hydroponic solutions of 2mM MgSO4*7H2O, 3mM Mg(NO3)2*6H2O, 2.5mM KNO3, 1mM CaCL2*2H2O, 4mM Ca(NO3)2*4H2O, 0.020mM KH2PO4, 542uM KOH, 217uM DTPA, 1.5uM MnCl2 *4H2O, 4.6uM ZnSO4*7H2O, 2uM CuSO4*5H2O, 0.2uM NaMoO4*2H2O, 1uM CoSO4*7H2O, 1uM NiSO4*6H2O, 10uM H3BO3, 20mM HCO3, and either 50 or 100uM Fe(NO3)3. A daily nutrient solution of 16mM KPO4, 0.287mM H3BO3, and 355mM NH4(NO3)3 maintained stable nutrient conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the TRIzol method, DNAse treated with Ambion DNA-free kit, then further purified using the RNeasy mini kit (QIAGEN)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
RNA samples were submited to the University of Minnesota BioMedical Genomics Centerfor hybridization to Soybean Affymetrix GeneChips
|
| Scan protocol |
GeneChips were scanned using the Genechip 3000 scanner
|
| Description |
Gene expression data from iron deficient IsoClark 10DAP
|
| Data processing |
Data was analyzed using the 'justRMA' command in R. Data was analyzed for 10DAP roots and 14DAP roots
|
| |
|
| Submission date |
Jun 08, 2010 |
| Last update date |
Sep 06, 2010 |
| Contact name |
Carroll P Vance |
| E-mail(s) |
vance004@umn.edu
|
| Phone |
612-625-5715
|
| Organization name |
USDA-ARS, University of Minnesota
|
| Department |
Agronomy and Plant Genetics
|
| Lab |
Vance
|
| Street address |
1991 Upper Buford Circle, 411 Borlaug Hall
|
| City |
St. Paul |
| State/province |
MN |
| ZIP/Postal code |
55108 |
| Country |
USA |
| |
|
| Platform ID |
GPL4592 |
| Series (1) |
| GSE22227 |
Expression data of Soybean (Glycine max) roots from different iron treatments. |
|
