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Sample GSM320469 Query DataSets for GSM320469
Status Public on Sep 16, 2008
Title protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: Mo17 maize inbred - rep2
Sample type genomic
 
Source name leaf (protocol: Amplified fragment restriction polymorphism (AFLP) - 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 Amplified fragment length polymorphism (AFLP)
Label biotin
Label protocol BioPrime DNA labeling system for AFLP
 
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description Plants grown in glasshouse for 2 weeks.
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 29400 P 0.000146616
AFFX-BioB-5_at 21951 P 5.16933e-05
AFFX-BioB-M_at 37535 P 0.000169266
AFFX-BioC-3_at 49067 P 4.43055e-05
AFFX-BioC-5_at 64786 P 4.43055e-05
AFFX-BioDn-3_at 214120 P 4.43055e-05
AFFX-BioDn-5_at 139220 P 5.16933e-05
AFFX-CreX-3_at 377760 P 4.43055e-05
AFFX-CreX-5_at 391240 P 5.16933e-05
AFFX-DapX-3_at 76.967 A 0.963431
AFFX-DapX-5_at 410.29 A 0.440646
AFFX-DapX-M_at 108.19 A 0.794268
AFFX-LysX-3_at 327.75 A 0.095667
AFFX-LysX-5_at 451.53 M 0.0629293
AFFX-LysX-M_at 82.809 A 0.966323
AFFX-PheX-3_at 426.28 A 0.876428
AFFX-PheX-5_at 401.81 A 0.699394
AFFX-PheX-M_at 70.48 A 0.957038
AFFX-r2-Bs-dap-3_at 309.39 A 0.0911573
AFFX-r2-Bs-dap-5_at 200.06 A 0.429432

Total number of rows: 17734

Table truncated, full table size 602 Kbytes.




Supplementary file Size Download File type/resource
GSM320469.CEL.gz 1.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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