|
| Status |
Public on Mar 26, 2009 |
| Title |
Mature Soybean (Glycine max) pollen grains Replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
Mature pollen grains from soybean
|
| Organism |
Glycine max |
| Characteristics |
Mature pollen grains
|
| Growth protocol |
The plants used for pollen collection were grown in a temperature controlled glasshouse with a 16 hour light / 8 hour dark photoperiod at 30 degrees C. They were grown in vermiculite with the addition of a slow release fertilizer (osmocote). When the plants had matured and developed significant biomass, flowering was induced by changing the photoperiod to 12 hours. Pollen was collected on cover slips by rubbing isolated anthers together, and non-pollen tissue was removed from cover slip prior to freezing at -80 degrees.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from various tissues was isolated using QIAGEN RNeasy Mini Kit (QIAGEN) according to the manufacturer's protocols and eluted with ultra pure nuclease-free water.
|
| Label |
biotin
|
| Label protocol |
Labelling and hybridization were performed according to the manufacturer's instructions (Affymetrix Inc.) by AGRF (Australian Genome Research Facility, Melbourne, Australia)
|
| |
|
| Hybridization protocol |
Labelling and hybridization were performed according to the manufacturer's instructions (Affymetrix Inc.) by AGRF (Australian Genome Research Facility, Melbourne, Australia)
|
| Scan protocol |
Labelling and hybridization were performed according to the manufacturer's instructions (Affymetrix Inc.) by AGRF (Australian Genome Research Facility, Melbourne, Australia)
|
| Description |
GeneChip Soybean Genome array (Affymetrix, Inc.) containing 37,500 unique transcript (probe) was used in this study. Three biological replicates for pollen and two biological replicates for sporophytic tissues were used
|
| Data processing |
AffylmGUI that is a graphical user interface for analysis of Affymetrix microarray data, was used for data analysis (http://www.r-project.org). Data normalization (Quantile normalization method) and expression measures were done using RMA (Robust Multiarray Averaging) algorithm (R package) [69, 70], differential expression and contrast analysis was performed using sporophytic (non-meristematic) tissues hybridized chips as the baseline [71]. We chose the p value cutoff of P ≤0.001( from t-test) and empirical bayes log odds of differential expression (B) to zero.
Hybridization quality was tested by checking the soybean control genes including 18S rRNA, Actin, GSTa, cytochrome P450, SBP, Ubiquitin, and GAPDH (spotted by the manufacturer). The expression ratios [P (-)/P (+)] of the control genes were consistently in the range of 0.16-2.84.
|
| |
|
| Submission date |
Jul 30, 2008 |
| Last update date |
Mar 26, 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) |
| GSE12286 |
Genomic Expression Profiling of Mature Soybean (Glycine max) Pollen |
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