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Sample GSM207566 Query DataSets for GSM207566
Status Public on Jul 02, 2008
Title Mudanjiang8 wild type control rep2
Sample type RNA
Source name Mudanjiang8 wild type control plant
Organism Oryza sativa
Characteristics Mudanjiang8 wild type control
Growth protocol Leaves of a 20 different plants pool were harvested from the 4-week old wild-type Mudanjiang 8 (Oryza sativa ssp. japonica) and OsWRKY13-overexpressing independent transgenic lines (D11UM1-1 and D11UM7-2) growing in the greenhouse at 26°C with 12 hours daylight. The experiment was repeated three times.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with TRIZOL reagent (Invitrogen, Gaithersburg, MD) and was further purified with Nucleospin RNA Clean-up Kit (Macherey-Nagel, Germany) according to the manufacture’s instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and concentration was quantitated by spectrophotometric analysis.
Label biotin
Label protocol Biotin labeled cRNA was produced with MessageAmp II-Biotin Kit (Ambion Inc., Texas) with 5 ug of total RNA as starting material for each sample reaction.
Hybridization protocol Fifteen micrograms of the resulting biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320) to probe sets on an Affymetrix Genechip Rice Genome Array.
Scan protocol The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix, Inc.).
Description Microsoft Excel program was used to merge the overlapping significant genes from two transgenic generations. Annotations from Affymetrix for significant genes were checked in NCBI public database using Blastx program (Altschul et al., 1997) and in TIGR Rice Genome Annotation version 4.0 (, Yuan et al., 2005) and corrected if necessary.
Data processing The results were quantified and normalized using MicroArray Suite 5.0 (GCOS1.4) software (Affymetrix, Inc.).The genes with probe set signal lower than 100 on the repeated six arrays were considered as non-expression and filtered out (Hu and Ma, 2006), resulting in 24283 expressed genes in rice line D11UM1-1 and 24293 expressed genes in D11UM7-2 for further analysis. The Significance Analysis of Microarrays (SAM) Excel Add-in (Tusher et al., 2001) was used to identify significantly differentially expressed genes between the control and OsWRKY13-overexpressing plants. The number of permutation for SAM analysis was 100. The delta value in the SAM was adjusted so that the estimated false discovery rate (FDR) was < 5% for significant genes. The cutoff value of expression fold change was set as 2.0 that was commonly used for microarray analysis to further increase the stringency (Hu and Ma, 2006).
Submission date Jul 05, 2007
Last update date Aug 14, 2011
Contact name Deyun Qiu
Phone 86-27-87281812
Fax 86-27-87287092
Organization name Huazhong Agricultural University
Department College of Life Science and Technology
Lab National Center of Plant Gene Research (Wuhan)
Street address Luoshi Road
City Wuhan
State/province Hubei
ZIP/Postal code 430070
Country China
Platform ID GPL2025
Series (1)
GSE8380 Rice Gene Network Inferred from Expression Profiling of Plants Overexpressing OsWRKY13

Data table header descriptions
VALUE average intensity of probe intensities for that gene from microarray (higher intensity = higher gene
ABS_CALL whether the Affymetrix data extraction software detected the mRNA for that gene or not (if detected, then
DETECTION P-VALUE P-value for confidence in ABS_CALL (from Affymetrix data extraction software)

Data table
AFFX-BioB-5_at 574.504 P 9.4506e-05
AFFX-BioB-M_at 609.014 P 4.42873e-05
AFFX-BioB-3_at 651.605 P 4.42873e-05
AFFX-BioC-5_at 1449.55 P 4.42873e-05
AFFX-BioC-3_at 1356.46 P 5.16732e-05
AFFX-BioDn-5_at 2501.61 P 4.42873e-05
AFFX-BioDn-3_at 6828.16 P 4.42873e-05
AFFX-CreX-5_at 17812.1 P 4.42873e-05
AFFX-CreX-3_at 23596.3 P 4.42873e-05
AFFX-DapX-5_at 600.097 P 5.16732e-05
AFFX-DapX-M_at 1425.22 P 5.16732e-05
AFFX-DapX-3_at 3798.98 P 4.42873e-05
AFFX-LysX-5_at 151.039 P 8.14279e-05
AFFX-LysX-M_at 197.506 P 0.000445901
AFFX-LysX-3_at 497.195 P 7.00668e-05
AFFX-PheX-5_at 286.891 P 7.00668e-05
AFFX-PheX-M_at 189.578 P 8.14279e-05
AFFX-PheX-3_at 430.899 P 0.00010954
AFFX-ThrX-5_at 193.437 P 5.16732e-05
AFFX-ThrX-M_at 506.378 P 4.42873e-05

Total number of rows: 57381

Table truncated, full table size 2175 Kbytes.

Supplementary file Size Download File type/resource
GSM207566.CEL.gz 4.4 Mb (ftp)(http) CEL
GSM207566.CHP.gz 317.4 Kb (ftp)(http) CHP
GSM207566.EXP.gz 499 b (ftp)(http) EXP
Raw data included within Sample table
Processed data included within Sample table
Raw data provided as supplementary file
Processed data provided as supplementary file

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