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Sample GSM267288 Query DataSets for GSM267288
Status Public on Feb 20, 2009
Title Axillary meristem from 10-day-old soybean seedlings repliacte 2
Sample type RNA
Source name vegetative axillary meristem
Organism Glycine max
Characteristics axillary meristem dissected from 10-day-old soybean plants grown under greenhouse conditions
Growth protocol Soybean plants [Glycine max. (L) Merr. Cv. Bragg] were grown in a greenhouse located at the University of Melbourne, Victoria, Australia.
Extracted molecule total RNA
Extraction protocol All RNA was extracted using using Qiagen RNeasy Mini Kit with on column DNAse digestion.
Label biotin
Label protocol cDNA labelling and Affymetrix Soybean GeneChip hybridization was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia)
Hybridization protocol DNA labelling and Affymetrix Soybean GeneChip hybridization was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia)
Scan protocol Carried out by AGRF according to standard protocol at
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 [78] 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 [78]. The list of transcripts that were detected to be differentially expressed at adjusted p-value of <0.05 was then filtered using a relatively conservative selection method. We applied a cut-off of a 1.5-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.
Submission date Feb 22, 2008
Last update date Feb 20, 2009
Contact name Chui E WONG
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

Data table header descriptions

Data table
AFFX-BioB-3_at 8.651764067
AFFX-BioB-5_at 8.77970976
AFFX-BioB-M_at 8.864798219
AFFX-BioC-3_at 9.989695978
AFFX-BioC-5_at 10.00892844
AFFX-BioDn-3_at 12.17737485
AFFX-BioDn-5_at 11.23993695
AFFX-CreX-3_at 13.6166691
AFFX-CreX-5_at 13.2725202
AFFX-DapX-3_at 9.607213044
AFFX-DapX-5_at 6.904812966
AFFX-DapX-M_at 9.139799339
AFFX-Gm_18SrRNA_at 11.68970447
AFFX-Gm_Actin_3_at 10.84658403
AFFX-Gm_Actin_5_at 5.084609723
AFFX-Gm_Actin_M_at 9.476601597
AFFX-Gm_GlutTrans_3_r_at 11.30414312
AFFX-Gm_GlutTrans_5_s_at 9.736935444
AFFX-Gm_GlutTrans_M_at 9.740955241
AFFX-Gm_P450_3_s_at 9.666662356

Total number of rows: 37776

Table truncated, full table size 1190 Kbytes.

Supplementary file Size Download File type/resource
GSM267288.CEL.gz 4.4 Mb (ftp)(http) CEL
GSM267288.CHP.gz 332.6 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table

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