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Sample GSM207560 Query DataSets for GSM207560
Status Public on Jul 02, 2008
Title Mudanjiang8 OsWRKY13 Overexpressing D11UM1-1 rep3
Sample type RNA
Source name Mudanjiang8 OsWRKY13 Overexpressing tansgenic plant D11UM1-1
Organism Oryza sativa
Characteristics OsWRKY13-overexpressing independent transgenic line T3 D11UM1-1
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 g 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 The results were quantified and normalized using MicroArray Suite 5.0 (GCOS1.4) software (Affymetrix, Inc.).
Data processing 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). 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.
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 expression)
ABS_CALL whether the Affymetrix data extraction software detected the mRNA for that gene or not (if detected, then P for Present; if not detected, then A for Absent; M is Marginal for borderline detection)
DETECTION P-VALUE P-value for confidence in ABS_CALL (from Affymetrix data extraction software)

Data table
AFFX-BioB-5_at 466.217 P 0.000146581
AFFX-BioB-M_at 614.086 P 4.42873e-05
AFFX-BioB-3_at 722.543 P 4.42873e-05
AFFX-BioC-5_at 1606.32 P 4.42873e-05
AFFX-BioC-3_at 1380.55 P 4.42873e-05
AFFX-BioDn-5_at 2769.79 P 4.42873e-05
AFFX-BioDn-3_at 7225.28 P 4.42873e-05
AFFX-CreX-5_at 18586 P 5.16732e-05
AFFX-CreX-3_at 26663.3 P 4.42873e-05
AFFX-DapX-5_at 552.923 P 4.42873e-05
AFFX-DapX-M_at 1328.2 P 7.00668e-05
AFFX-DapX-3_at 3460.25 P 4.42873e-05
AFFX-LysX-5_at 100.657 P 0.000296381
AFFX-LysX-M_at 184.74 P 0.000753643
AFFX-LysX-3_at 378.628 P 4.42873e-05
AFFX-PheX-5_at 209.564 P 0.000146581
AFFX-PheX-M_at 214.519 P 0.000146581
AFFX-PheX-3_at 319.989 P 0.000146581
AFFX-ThrX-5_at 136.037 P 0.000662269
AFFX-ThrX-M_at 407.97 P 4.42246e-05

Total number of rows: 57381

Table truncated, full table size 2173 Kbytes.

Supplementary file Size Download File type/resource
GSM207560.CEL.gz 4.4 Mb (ftp)(http) CEL
GSM207560.CHP.gz 316.3 Kb (ftp)(http) CHP
GSM207560.EXP.gz 498 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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