|
| Status |
Public on Feb 20, 2009 |
| Title |
Soy_non-shoot apical meristem2 |
| Sample type |
RNA |
| |
|
| Source name |
non-apical- meristem (NM) tissue consisted of primary stem, primary roots and mature leaves
|
| Organism |
Glycine max |
| Characteristics |
Cultivar Bragg. 10-day-old plants grown under the greenhouse condition in the University of Melbourne
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted using Qiagen RNAEasy Mini Kit
|
| Label |
Biotin
|
| Label protocol |
cDNA labelling and Affymetrix Soybean GeneChip hybridization was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia) 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) using 3 µg of total RNA.
|
| 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; Wettenhall & Smyth, 2004) 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 (Wettenhall & Smyth, 2004). The list of transcripts that were detected to be differentially expressed at adjusted p-value of <0.01 was then filtered using a relatively conservative selection method. We applied a cut-off of a 2-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. Hybridization quality was also tested by checking the expression level of the soybean housekeeping control genes that include 18S rRNA, Actin, GSTa, cytochrome P450, SBP, Ubiquitin, and GAPDH. The expression ratios (SAM/NM) of the control genes were consistently in the range of 0.83–1.29.
|
| |
|
| Submission date |
Oct 11, 2007 |
| Last update date |
Aug 14, 2011 |
| 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 |
|
