|
| Status |
Public on Apr 15, 2008 |
| Title |
Soybean-2601R-4-RMA |
| Sample type |
RNA |
| |
|
| Source name |
Soybean strain 2601R
|
| Organism |
Glycine max |
| Characteristics |
Strain: 2601R
Growth Stage: V2
|
| Biomaterial provider |
First Line Seeds Ltd., Guelph, ON, Canada
|
| Growth protocol |
Grown in growth changers in ambient humidity, 16h photoperiod, and 25/19°C day/night temperatures. 10 seeds sown into two 20 cm pots.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At the V2 growth stage (Fehr et al. 1971), completely unrolled first trifoliate leaves were harvested by cutting the petiole a few millimeters below the leaflets, immediately frozen in liquid nitrogen and stored at -80°C. RNA was extracted using the RNeasy Plant Mini Kit (Quiagen, Valencia, CA).
|
| Label |
biotin
|
| Label protocol |
5µg of total RNA was used to generate double-stranded cDNA using a T7-linked oligo(dT) primer and SuperScript II reverse transcriptase (Invitrogen) following the instructions for the One cycle-cDNA synthesis kit (from Affymetrix). cRNA were synthesized using the IVT labelling kit from Affymetrix, resulting in biotinylated cRNA.
|
| |
|
| Hybridization protocol |
Target preparation, hybridization and scanning were carried out at the McGill University and Genome Quebec Innovation Centre Microarray platform using the protocol recommended by Affymetrix (). Labelled cRNA were cleaned and fragmented using the Sample Cleanup Module reagents (Qiagen). Spike controls B2, bio-B, bio-C, bio-D, and Cre-x were added to the hybridization cocktail before overnight hybridization at 45°C for 16 h.
|
| Scan protocol |
Arrays were washed and stained in an Affymetrix fluidics Station prior to scanning on the GeneChip Scanner 3000 (Affymetrix). Image acquisition and processing was done with the Microarray Analysis Suite 5.0 (Affymetrix).
|
| Description |
Sample 4 from the 2601R soybean strain. The third of five samples for this strain.
|
| Data processing |
R and the BioConductor packages (Gentleman et al., 2004) such as affy, limma, cluster, and made4 were used for data analysis. This sample was pre-processed using the RMA method.
|
| |
|
| Submission date |
Oct 17, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Martina Stromvik |
| E-mail(s) |
[email protected]
|
| Phone |
+1 (514) 398 8627
|
| Fax |
+1 (514) 398 7897
|
| URL |
http://www.mcgill.ca/plant/faculty/stromvik/
|
| Organization name |
McGill University
|
| Department |
Department of Plant Science
|
| Lab |
Plant Bioinformatics
|
| Street address |
21,111 Lakeshore Rd
|
| City |
Ste-Anne-de-Bellevue |
| State/province |
Quebec |
| ZIP/Postal code |
H9X 3V9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL4592 |
| Series (1) |
| GSE9374 |
Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans |
|
