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Sample GSM421692 Query DataSets for GSM421692
Status Public on Jun 25, 2009
Title XOO, 4 hai - rep2
Sample type RNA
Source name shoot, XOO, 4 hai
Organism Oryza sativa
Characteristics germplasm name: cv. nipponbare
organism part: PO:0009006 shoot
development stage: PO:0007106 LP.03 three leaves visible
age: 2 weeks after sowing
growth media: LC-1 Soil Mix
Extracted molecule total RNA
Extraction protocol Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up
Label biotin
Label protocol Affy-Eukaryotic Target Preparation
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description R2XOO4H
Replication 2, Xoo-inoculated rice, tissue collected at 4HAI
Data processing The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor ( The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at The normalization scripts are available from the PLEXdb team by request.
Submission date Jun 24, 2009
Last update date Jun 25, 2009
Contact name PLEXdb Curator, Sudhansu Dash
Organization name Iowa State University
Department Virtual Reality Application Center
Lab PLEXdb
Street address 1023 Crop Genomes Informatics Lab (Iowa State University)
City Ames
State/province IA
ZIP/Postal code 50011
Country USA
Platform ID GPL2025
Series (1)
GSE16793 Comparative transcriptional profiling of rice undergoing infection by X. oryzae pv. oryzae or by X. oryzae pv. oryzicola

Data table header descriptions
ID_REF Affymetrix probe set id
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
AFFX-BioB-3_at 736.39 P 4.43055e-05
AFFX-BioB-5_at 742.95 P 0.000126831
AFFX-BioB-M_at 588.9 P 4.43055e-05
AFFX-BioC-3_at 2045.7 P 4.43055e-05
AFFX-BioC-5_at 1977.5 P 4.43055e-05
AFFX-BioDn-3_at 8825.2 P 4.43055e-05
AFFX-BioDn-5_at 3977.6 P 4.43055e-05
AFFX-CreX-3_at 27852 P 4.43055e-05
AFFX-CreX-5_at 23723 P 5.16933e-05
AFFX-DapX-3_at 4116.7 P 4.43055e-05
AFFX-DapX-5_at 1692.7 P 4.43055e-05
AFFX-DapX-M_at 2546.9 P 7.00908e-05
AFFX-LysX-3_at 682.05 P 5.16933e-05
AFFX-LysX-5_at 182.09 P 4.43055e-05
AFFX-LysX-M_at 307.64 P 0.00110204
AFFX-Mgr-actin-3_at 4.1593 A 0.856998
AFFX-Mgr-actin-5_at 49.579 A 0.266847
AFFX-Mgr-actin-M_at 5.3875 A 0.95442
AFFX-Mgr-ef1a-3_at 10.688 A 0.605162
AFFX-Mgr-ef1a-3_x_at 10.526 A 0.788202

Total number of rows: 57381

Table truncated, full table size 2104 Kbytes.

Supplementary file Size Download File type/resource
GSM421692.CEL.gz 4.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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