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Sample GSM421679 Query DataSets for GSM421679
Status Public on Jun 25, 2009
Title XOC, 24 hai - rep1
Sample type RNA
Source name shoot, XOC, 24 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 R1XOC24H
Replication 1, Xoc-inoculated rice, tissue collected at 24HAI
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 705.94 P 4.43055e-05
AFFX-BioB-5_at 823.54 P 0.000258404
AFFX-BioB-M_at 633.75 P 7.00908e-05
AFFX-BioC-3_at 2051.2 P 5.16933e-05
AFFX-BioC-5_at 1986 P 4.43055e-05
AFFX-BioDn-3_at 9459.8 P 4.43055e-05
AFFX-BioDn-5_at 3493.4 P 4.43055e-05
AFFX-CreX-3_at 28745 P 4.43055e-05
AFFX-CreX-5_at 25773 P 5.16933e-05
AFFX-DapX-3_at 5014.3 P 5.16933e-05
AFFX-DapX-5_at 1821.5 P 4.43055e-05
AFFX-DapX-M_at 3180.2 P 9.45344e-05
AFFX-LysX-3_at 934.49 P 7.00908e-05
AFFX-LysX-5_at 240.96 P 6.0233e-05
AFFX-LysX-M_at 476.06 P 0.000972217
AFFX-Mgr-actin-3_at 5.391 A 0.835968
AFFX-Mgr-actin-5_at 51.524 A 0.5
AFFX-Mgr-actin-M_at 9.6912 A 0.835968
AFFX-Mgr-ef1a-3_at 29.864 A 0.464576
AFFX-Mgr-ef1a-3_x_at 10.293 A 0.835968

Total number of rows: 57381

Table truncated, full table size 2097 Kbytes.

Supplementary file Size Download File type/resource
GSM421679.CEL.gz 4.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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