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Sample GSM320472 Query DataSets for GSM320472
Status Public on Sep 16, 2008
Title protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred - rep2
Sample type genomic
 
Source name leaf (protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred)
Organism Zea mays
Characteristics CML69 (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 14833 P 0.000972217
AFFX-BioB-5_at 9656.5 P 4.43055e-05
AFFX-BioB-M_at 17252 P 0.000662332
AFFX-BioC-3_at 25997 P 5.16933e-05
AFFX-BioC-5_at 36772 P 4.43055e-05
AFFX-BioDn-3_at 114050 P 4.43055e-05
AFFX-BioDn-5_at 76663 P 7.00908e-05
AFFX-CreX-3_at 225680 P 4.43055e-05
AFFX-CreX-5_at 225240 P 5.16933e-05
AFFX-DapX-3_at 74.726 A 0.971543
AFFX-DapX-5_at 200.92 A 0.724854
AFFX-DapX-M_at 208.88 A 0.772364
AFFX-LysX-3_at 148.2 A 0.574038
AFFX-LysX-5_at 120.48 A 0.559354
AFFX-LysX-M_at 105.09 A 0.937071
AFFX-PheX-3_at 421.83 A 0.868639
AFFX-PheX-5_at 141.45 A 0.659339
AFFX-PheX-M_at 237.39 A 0.712257
AFFX-r2-Bs-dap-3_at 63.997 A 0.570568
AFFX-r2-Bs-dap-5_at 143.81 A 0.535424

Total number of rows: 17734

Table truncated, full table size 604 Kbytes.




Supplementary file Size Download File type/resource
GSM320472.CEL.gz 2.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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