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Sample GSM308559 Query DataSets for GSM308559
Status Public on Mar 26, 2009
Title Mature Soybean (Glycine max) pollen grains Replicate 2
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

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
GmaAffx.21929.1.S1_at 15.64870722
GmaAffx.67513.1.S1_at 15.58282194
GmaAffx.9455.1.S1_at 15.56733242
GmaAffx.78316.1.S1_at 15.51308529
GmaAffx.43840.1.S1_at 15.44486564
GmaAffx.57996.1.S1_at 15.45906806
GmaAffx.63015.1.S1_at 15.45037864
GmaAffx.79807.1.S1_at 15.40010629
GmaAffx.66571.1.S1_at 15.40199795
Gma.6551.1.S1_s_at 15.42470065
GmaAffx.71146.1.S1_at 15.27837162
Gma.10101.1.S1_at 15.22560115
Gma.5077.1.A1_at 15.23764861
Gma.6327.1.S1_s_at 15.27165217
GmaAffx.26070.1.S1_at 15.23846282
Gma.825.1.A1_at 15.22426343
GmaAffx.58015.1.S1_at 15.26111807
GmaAffx.53728.1.S1_at 15.1764649
GmaAffx.12889.1.S1_at 15.11352996
GmaAffx.78268.1.S1_at 15.05514017

Total number of rows: 37593

Table truncated, full table size 1184 Kbytes.




Supplementary file Size Download File type/resource
GSM308559.CEL.gz 4.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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