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Sample GSM421701 Query DataSets for GSM421701
Status Public on Jun 25, 2009
Title XOO, 24 hai - rep3
Sample type RNA
Source name shoot, XOO, 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 R3XOO24H
Replication 3, Xoo-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 882.16 P 4.43055e-05
AFFX-BioB-5_at 1010.3 P 0.000195157
AFFX-BioB-M_at 788.59 P 5.16933e-05
AFFX-BioC-3_at 2587.5 P 4.43055e-05
AFFX-BioC-5_at 2615.3 P 5.16933e-05
AFFX-BioDn-3_at 10419 P 4.43055e-05
AFFX-BioDn-5_at 4919.3 P 4.43055e-05
AFFX-CreX-3_at 36496 P 4.43055e-05
AFFX-CreX-5_at 29576 P 5.16933e-05
AFFX-DapX-3_at 4678.1 P 4.43055e-05
AFFX-DapX-5_at 2198.4 P 4.43055e-05
AFFX-DapX-M_at 3275.9 P 8.1454e-05
AFFX-LysX-3_at 807.71 P 5.16933e-05
AFFX-LysX-5_at 248.53 P 4.43055e-05
AFFX-LysX-M_at 426.99 P 0.000389851
AFFX-Mgr-actin-3_at 10.31 A 0.813028
AFFX-Mgr-actin-5_at 33.545 A 0.638946
AFFX-Mgr-actin-M_at 40.887 A 0.5
AFFX-Mgr-ef1a-3_at 46.45 A 0.361054
AFFX-Mgr-ef1a-3_x_at 16.273 A 0.638946

Total number of rows: 57381

Table truncated, full table size 2100 Kbytes.

Supplementary file Size Download File type/resource
GSM421701.CEL.gz 4.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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