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Sample GSM421686 Query DataSets for GSM421686
Status Public on Jun 25, 2009
Title XOC, 96 hai - rep4
Sample type RNA
Source name shoot, XOC, 96 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 R4XOC96H
Replication 4, Xoc-inoculated rice, tissue collected at 96HAI
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 536.06 P 4.43055e-05
AFFX-BioB-5_at 491.94 P 0.000224712
AFFX-BioB-M_at 452.3 P 4.43055e-05
AFFX-BioC-3_at 1257.8 P 4.43055e-05
AFFX-BioC-5_at 1349.9 P 4.43055e-05
AFFX-BioDn-3_at 7662.9 P 4.43055e-05
AFFX-BioDn-5_at 3185 P 4.43055e-05
AFFX-CreX-3_at 21359 P 4.43055e-05
AFFX-CreX-5_at 20190 P 4.43055e-05
AFFX-DapX-3_at 4577.6 P 4.43055e-05
AFFX-DapX-5_at 1943.6 P 4.43055e-05
AFFX-DapX-M_at 2367.3 P 7.00908e-05
AFFX-LysX-3_at 489.92 P 4.43055e-05
AFFX-LysX-5_at 179.47 P 4.43055e-05
AFFX-LysX-M_at 300.41 P 0.000753709
AFFX-Mgr-actin-3_at 2.3883 A 0.945245
AFFX-Mgr-actin-5_at 11.266 A 0.893388
AFFX-Mgr-actin-M_at 19.174 A 0.671679
AFFX-Mgr-ef1a-3_at 43.454 A 0.605162
AFFX-Mgr-ef1a-3_x_at 50.908 A 0.535424

Total number of rows: 57381

Table truncated, full table size 2103 Kbytes.

Supplementary file Size Download File type/resource
GSM421686.CEL.gz 4.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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