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Sample GSM320450 Query DataSets for GSM320450
Status Public on Sep 16, 2008
Title protocol: Cot filtration (CF) - genotype: Mo17 maize inbred - rep1
Sample type genomic
 
Source name leaf (protocol: Cot filtration (CF) - genotype: Mo17 maize inbred)
Organism Zea mays
Characteristics Mo17 (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007134 A vegetative growth, PO:0007071 2.02 main shoot and axillary shoots visible at two nodes (Development Stage); 2 week old (Age); Scotts MetroMix 200 (Growth Media).
Growth protocol Growth Description: glasshouse
Extracted molecule genomic DNA
Extraction protocol Cot Filtration (CF)
Label biotin
Label protocol BioPrime DNA labeling system for CF/MF
 
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description Plants grown in glasshouse for 2 weeks. Array data is low quality. The data has low correlation (0.5) with other Mo17-CF arrays.
Data processing The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). 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 http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.
 
Submission date Sep 13, 2008
Last update date Sep 15, 2008
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 GPL4032
Series (1)
GSE12770 Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes

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
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-3_at 483.67 P 0.0284572
AFFX-BioB-5_at 520.61 P 0.000662332
AFFX-BioB-M_at 685.74 P 0.000753709
AFFX-BioC-3_at 964.63 P 0.000389851
AFFX-BioC-5_at 1292.1 P 0.000195157
AFFX-BioDn-3_at 4230.8 P 5.16933e-05
AFFX-BioDn-5_at 2879.8 P 8.1454e-05
AFFX-CreX-3_at 8443.3 P 4.43055e-05
AFFX-CreX-5_at 7513.1 P 5.16933e-05
AFFX-DapX-3_at 61.945 A 0.216524
AFFX-DapX-5_at 53.567 A 0.0780018
AFFX-DapX-M_at 10.795 A 0.794268
AFFX-LysX-3_at 4.123 A 0.52976
AFFX-LysX-5_at 5.1328 A 0.631562
AFFX-LysX-M_at 16.747 A 0.9273
AFFX-PheX-3_at 29.235 A 0.794268
AFFX-PheX-5_at 30.36 A 0.631562
AFFX-PheX-M_at 8.7016 A 0.772364
AFFX-r2-Bs-dap-3_at 7.443 A 0.328321
AFFX-r2-Bs-dap-5_at 5.6477 A 0.945245

Total number of rows: 17734

Table truncated, full table size 635 Kbytes.




Supplementary file Size Download File type/resource
GSM320450.CEL.gz 2.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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