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Sample GSM421709 Query DataSets for GSM421709
Status Public on Jun 25, 2009
Title MOCK, 2 hai - rep3
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 R3MOCK2H
Replication 3, 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 637.22 P 5.16933e-05
AFFX-BioB-5_at 776.67 P 0.000296757
AFFX-BioB-M_at 556.97 P 6.0233e-05
AFFX-BioC-3_at 1920.2 P 4.43055e-05
AFFX-BioC-5_at 2040.6 P 5.16933e-05
AFFX-BioDn-3_at 9189.6 P 4.43055e-05
AFFX-BioDn-5_at 3610.8 P 4.43055e-05
AFFX-CreX-3_at 27889 P 4.43055e-05
AFFX-CreX-5_at 25013 P 5.16933e-05
AFFX-DapX-3_at 4004.3 P 5.16933e-05
AFFX-DapX-5_at 1673.3 P 4.43055e-05
AFFX-DapX-M_at 2629.3 P 7.00908e-05
AFFX-LysX-3_at 672.11 P 4.43055e-05
AFFX-LysX-5_at 252.32 P 4.43055e-05
AFFX-LysX-M_at 358.42 P 0.00159264
AFFX-Mgr-actin-3_at 4.321 A 0.893388
AFFX-Mgr-actin-5_at 32.384 A 0.638946
AFFX-Mgr-actin-M_at 12.133 A 0.835968
AFFX-Mgr-ef1a-3_at 15.648 A 0.703144
AFFX-Mgr-ef1a-3_x_at 64.044 A 0.605162

Total number of rows: 57381

Table truncated, full table size 2100 Kbytes.

Supplementary file Size Download File type/resource
GSM421709.CEL.gz 4.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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