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Sample GSM258498 Query DataSets for GSM258498
Status Public on Jan 17, 2009
Title Soybean shoot apical meristem, 2 short-day treatment
Sample type RNA
 
Source name shoot apical meristem micro-dissected from 2 short-day treated soybean plants
Organism Glycine max
Characteristics hoot apical meristem micro-dissected from 10-day-old soybean plants that has been subjected to 2 complete short-day cycles.
Treatment protocol Soybean plants [Glycine max. (L) Merr. Cv. Bragg] were grown from seeds in a greenhouse located at the University of Melbourne, Victoria, Australia for 10 days before being shifted to growth chamber (short-day treatment) under a 10-hour light regime (100 µmol m-2 s-1) maintained at a constant temperature of 24°C.
Growth protocol Soybean plants [Glycine max. (L) Merr. Cv. Bragg] were grown from seeds in a greenhouse located at the University of Melbourne, Victoria, Australia for 10 days and then shifted to short-day growth chamber for short-day treatment.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from dissected SAMs using Qiagen RNeasy Mini Kit with on-column DNAse digestion (Qiagen Pty Ltd, Victoria, Australia).
Label Biotin
Label protocol cDNA labelling and Affymetrix Soybean GeneChip hybridization was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia) according to protocol provided by Affymetrix 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) according to protocol provided by Affymetrix using 3 µg of total RNA.
Scan protocol Scanning of the arrays was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia) according to protocol provided by Affymetrix.
Description This experiment consists of 5 samples with two biological replicates ( a total of 10 arrays)
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 filtered so that genes with expression levels that were called as “Marginal” or “Absence” in all 10 arrays according to the Affymetrix Statistical Algorithms were excluded from further analysis. The resulting data were then normalized using Robust Multiarray Averaging (RMA) implemented in AffylmGUI (Wettenhall and Smyth, 2004) and then imported into maSigPro, a statistical method employing a two-step regression approach (Conesa et al., 2006). For the first regression model, the p value is set at <0.05 while in the second regression step, a backward method was selected. A combination of quadratic and cubic model was used to evaluate significantly differential expression profiles in the process.
 
Submission date Jan 23, 2008
Last update date Jan 17, 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)
GSE10251 Gene expression profiling implicates novel hormonal regulation of the floral initiation process in soybeans

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
AFFX-BioB-3_at 7.837480281
AFFX-BioB-5_at 8.237691908
AFFX-BioB-M_at 8.053001201
AFFX-BioC-3_at 9.263605475
AFFX-BioC-5_at 9.160547218
AFFX-BioDn-3_at 11.42327716
AFFX-BioDn-5_at 10.62560077
AFFX-CreX-3_at 13.50046043
AFFX-CreX-5_at 13.11580764
AFFX-DapX-3_at 11.49868996
AFFX-DapX-5_at 10.29439203
AFFX-DapX-M_at 11.33359491
AFFX-Gm_18SrRNA_at 7.890460725
AFFX-Gm_Actin_3_at 11.78685392
AFFX-Gm_Actin_5_at 5.269948886
AFFX-Gm_Actin_M_at 10.39189296
AFFX-Gm_GlutTrans_3_r_at 11.73333072
AFFX-Gm_GlutTrans_5_s_at 10.19085705
AFFX-Gm_GlutTrans_M_at 10.27907766
AFFX-Gm_P450_3_s_at 8.732647014

Total number of rows: 37746

Table truncated, full table size 1189 Kbytes.




Supplementary file Size Download File type/resource
GSM258498.CEL.gz 5.1 Mb (ftp)(http) CEL
GSM258498.CHP.gz 325.5 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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