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Sample GSM238054 Query DataSets for GSM238054
Status Public on Apr 15, 2008
Title Soybean-PS46R-3-RMA
Sample type RNA
 
Source name Soybean strain PS46R
Organism Glycine max
Characteristics Strain: PS46R
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 3 from the PS46R 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) martina.stromvik@mcgill.ca
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

Data table header descriptions
ID_REF
VALUE RMA normalized values for each probe
SCALE logarithmic scale for VALUE

Data table
ID_REF VALUE SCALE
AFFX-BioB-3_at 6.67105258329147 log2
AFFX-BioB-5_at 7.07257746724799 log2
AFFX-BioB-M_at 7.1837706267477 log2
AFFX-BioC-3_at 8.56515534749314 log2
AFFX-BioC-5_at 8.13435601185105 log2
AFFX-BioDn-3_at 10.8144469622872 log2
AFFX-BioDn-5_at 10.0214884432582 log2
AFFX-CreX-3_at 12.2629331743978 log2
AFFX-CreX-5_at 11.7780286631252 log2
AFFX-DapX-3_at 8.17017395838263 log2
AFFX-DapX-5_at 6.40178481594327 log2
AFFX-DapX-M_at 7.38011456084711 log2
AFFX-Gm_18SrRNA_at 4.53742844975605 log2
AFFX-Gm_Actin_3_at 9.04871121711154 log2
AFFX-Gm_Actin_5_at 2.23470274473702 log2
AFFX-Gm_Actin_M_at 6.54212715487354 log2
AFFX-Gm_GlutTrans_3_r_at 10.1531650832318 log2
AFFX-Gm_GlutTrans_5_s_at 9.1245705436858 log2
AFFX-Gm_GlutTrans_M_at 9.84513028766197 log2
AFFX-Gm_P450_3_s_at 6.22341843739003 log2

Total number of rows: 61170

Table truncated, full table size 2538 Kbytes.




Supplementary file Size Download File type/resource
GSM238054.CEL.gz 7.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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