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Sample GSM421706 Query DataSets for GSM421706
Status Public on Jun 25, 2009
Title XOO, 96 hai - rep4
Sample type RNA
Source name shoot, XOO, 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 R4XOO96H
Replication 4, Xoo-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 337.7 P 4.43055e-05
AFFX-BioB-5_at 474.31 P 0.000509474
AFFX-BioB-M_at 345.53 P 7.00908e-05
AFFX-BioC-3_at 927.45 P 4.43055e-05
AFFX-BioC-5_at 1166.5 P 4.43055e-05
AFFX-BioDn-3_at 5857.3 P 4.43055e-05
AFFX-BioDn-5_at 2437.2 P 4.43055e-05
AFFX-CreX-3_at 17279 P 4.43055e-05
AFFX-CreX-5_at 14399 P 4.43055e-05
AFFX-DapX-3_at 4844.2 P 4.43055e-05
AFFX-DapX-5_at 2067.3 P 5.16933e-05
AFFX-DapX-M_at 2319.9 P 8.1454e-05
AFFX-LysX-3_at 397.07 P 6.0233e-05
AFFX-LysX-5_at 159.92 P 0.000195157
AFFX-LysX-M_at 375.71 P 0.00286705
AFFX-Mgr-actin-3_at 3.2944 A 0.908843
AFFX-Mgr-actin-5_at 17.878 A 0.788202
AFFX-Mgr-actin-M_at 9.2408 A 0.788202
AFFX-Mgr-ef1a-3_at 20.108 A 0.733153
AFFX-Mgr-ef1a-3_x_at 90.615 A 0.5

Total number of rows: 57381

Table truncated, full table size 2100 Kbytes.

Supplementary file Size Download File type/resource
GSM421706.CEL.gz 4.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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