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Sample GSM421708 Query DataSets for GSM421708
Status Public on Jun 25, 2009
Title MOCK, 2 hai - rep2
Sample type RNA
Source name shoot, MOCK, 2 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 R2MOCK2H
Replication 2, Mock-inoculated rice, tissue collected at 2HAI
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 653.84 P 4.43055e-05
AFFX-BioB-5_at 688.89 P 0.000169266
AFFX-BioB-M_at 629.99 P 5.16933e-05
AFFX-BioC-3_at 2134.5 P 4.43055e-05
AFFX-BioC-5_at 2152.6 P 4.43055e-05
AFFX-BioDn-3_at 9439.6 P 4.43055e-05
AFFX-BioDn-5_at 3794.6 P 4.43055e-05
AFFX-CreX-3_at 28102 P 4.43055e-05
AFFX-CreX-5_at 25022 P 5.16933e-05
AFFX-DapX-3_at 4246.3 P 5.16933e-05
AFFX-DapX-5_at 1954.5 P 4.43055e-05
AFFX-DapX-M_at 2642.1 P 7.00908e-05
AFFX-LysX-3_at 729.41 P 6.0233e-05
AFFX-LysX-5_at 193.44 P 4.43055e-05
AFFX-LysX-M_at 400 P 0.00286705
AFFX-Mgr-actin-3_at 4.4437 A 0.876127
AFFX-Mgr-actin-5_at 15.559 A 0.703144
AFFX-Mgr-actin-M_at 8.8663 A 0.761547
AFFX-Mgr-ef1a-3_at 49.581 A 0.570568
AFFX-Mgr-ef1a-3_x_at 5.9488 A 0.813028

Total number of rows: 57381

Table truncated, full table size 2103 Kbytes.

Supplementary file Size Download File type/resource
GSM421708.CEL.gz 4.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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