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Sample GSM320468 Query DataSets for GSM320468
Status Public on Sep 16, 2008
Title protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: Mo17 maize inbred - rep1
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 12910 P 0.000972217
AFFX-BioB-5_at 10041 P 7.00908e-05
AFFX-BioB-M_at 14685 P 0.00179598
AFFX-BioC-3_at 23672 P 5.16933e-05
AFFX-BioC-5_at 29306 P 4.43055e-05
AFFX-BioDn-3_at 108770 P 4.43055e-05
AFFX-BioDn-5_at 67202 P 8.1454e-05
AFFX-CreX-3_at 218240 P 4.43055e-05
AFFX-CreX-5_at 224010 P 5.16933e-05
AFFX-DapX-3_at 87.219 A 0.984817
AFFX-DapX-5_at 148.36 A 0.455412
AFFX-DapX-M_at 107.96 A 0.804734
AFFX-LysX-3_at 84.718 A 0.783476
AFFX-LysX-5_at 107.07 A 0.47024
AFFX-LysX-M_at 187.03 A 0.737173
AFFX-PheX-3_at 444.82 A 0.783476
AFFX-PheX-5_at 85.544 A 0.712257
AFFX-PheX-M_at 70.301 A 0.953518
AFFX-r2-Bs-dap-3_at 101.21 A 0.429432
AFFX-r2-Bs-dap-5_at 230.43 A 0.535424

Total number of rows: 17734

Table truncated, full table size 602 Kbytes.




Supplementary file Size Download File type/resource
GSM320468.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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