|
| Status |
Public on Jan 17, 2009 |
| Title |
Vegetative shoot apical meristem, replicate B |
| Sample type |
RNA |
| |
|
| Source name |
soybean shoot apical meristem, vegetative
|
| Organism |
Glycine max |
| Characteristics |
Vegetative shoot apical meristem micro-dissected from 10-day-old soybean plants under the dissecting microscope at 40x magnification
|
| Treatment protocol |
Soybean plants [Glycine max. (L) Merr. Cv. Bragg] were grown from seeds in a greenhouse located at the University of Melbourne, Victoria, Australia for 10 days before being shifted to growth chamber (short-day treatment) under a 10-hour light regime (100 µmol m-2 s-1) maintained at a constant temperature of 24°C.
|
| Growth protocol |
Soybean plants [Glycine max. (L) Merr. Cv. Bragg] were grown from seeds in a greenhouse located at the University of Melbourne, Victoria, Australia for 10 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from dissected SAMs using Qiagen RNeasy Mini Kit with on-column DNAse digestion (Qiagen Pty Ltd, Victoria, Australia).
|
| Label |
Biotin
|
| Label protocol |
cDNA labelling and Affymetrix Soybean GeneChip hybridization was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia) according to protocol provided by Affymetrix using 3 µg of total RNA.
|
| |
|
| Hybridization protocol |
cDNA labelling and Affymetrix Soybean GeneChip hybridization was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia) according to protocol provided by Affymetrix using 3 µg of total RNA.
|
| Scan protocol |
Scanning of the arrays was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia) according to protocol provided by Affymetrix.
|
| Description |
This experiment consists of 5 samples with two biological replicates ( a total of 10 arrays)
|
| Data processing |
Expression levels were estimated from Affymetrix hybridization intensity data using MicroArray Suite 5.0 (Affymetrix 2001). Raw numeric values representing the signal of each feature were filtered so that genes with expression levels that were called as “Marginal” or “Absence” in all 10 arrays according to the Affymetrix Statistical Algorithms were excluded from further analysis. The resulting data were then normalized using Robust Multiarray Averaging (RMA) implemented in AffylmGUI (Wettenhall and Smyth, 2004) and then imported into maSigPro, a statistical method employing a two-step regression approach (Conesa et al., 2006). For the first regression model, the p value is set at <0.05 while in the second regression step, a backward method was selected. A combination of quadratic and cubic model was used to evaluate significantly differential expression profiles in the process.
|
| |
|
| Submission date |
Jan 23, 2008 |
| Last update date |
Jan 17, 2009 |
| Contact name |
Chui E WONG |
| E-mail(s) |
acewong@unimelb.edu.au
|
| Organization name |
University of Melbourne
|
| Department |
Land and Food
|
| Lab |
Plant Molecular Biology and Biotechnology Group
|
| Street address |
University of Melbourne
|
| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL4592 |
| Series (1) |
| GSE10251 |
Gene expression profiling implicates novel hormonal regulation of the floral initiation process in soybeans |
|
