|
| Status |
Public on Feb 20, 2009 |
| Title |
Axillary meristem from 10-day-old soybean seedlings repliacte 2 |
| Sample type |
RNA |
| |
|
| Source name |
vegetative axillary meristem
|
| Organism |
Glycine max |
| Characteristics |
axillary meristem dissected from 10-day-old soybean plants grown under greenhouse conditions
|
| Growth protocol |
Soybean plants [Glycine max. (L) Merr. Cv. Bragg] were grown in a greenhouse located at the University of Melbourne, Victoria, Australia.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All RNA was extracted using using Qiagen RNeasy Mini Kit with on column DNAse digestion.
|
| Label |
biotin
|
| Label protocol |
cDNA labelling and Affymetrix Soybean GeneChip hybridization was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia)
|
| |
|
| Hybridization protocol |
DNA labelling and Affymetrix Soybean GeneChip hybridization was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia)
|
| Scan protocol |
Carried out by AGRF according to standard protocol at www.affymetrix.com
|
| Description |
Two independent biological replicates were used in the experiment
|
| 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 imported into AffylmGUI (Affymetrix linear modeling Graphical User Interface [78] for linear modeling of the microarray data and for identifying differentially expressed genes in SAMs. The data was normalized using Robust Multiarray Averaging (RMA) method and a linear model was then used to average data between replicate arrays and to look for variability between them [78]. The list of transcripts that were detected to be differentially expressed at adjusted p-value of <0.05 was then filtered using a relatively conservative selection method. We applied a cut-off of a 1.5-fold ratio of expression and filtered out those genes with expression levels that were called as “Marginal” or “Absence” in all six arrays according to the Affymetrix Statistical Algorithms.
|
| |
|
| Submission date |
Feb 22, 2008 |
| Last update date |
Feb 20, 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) |
| GSE10607 |
Genome-wide analysis of gene expression in the soybean shoot apical meristem |
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