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Sample GSM320455 Query DataSets for GSM320455
Status Public on Sep 16, 2008
Title protocol: Cot filtration (CF) - genotype: CML69 maize inbred - rep3
Sample type genomic
 
Source name leaf (protocol: Cot filtration (CF) - 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 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.
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 684.95 P 0.00359463
AFFX-BioB-5_at 452.74 P 0.000195157
AFFX-BioB-M_at 718.58 P 0.000224712
AFFX-BioC-3_at 1066.6 P 0.000258404
AFFX-BioC-5_at 1570.1 P 0.000146616
AFFX-BioDn-3_at 4399.5 P 4.43055e-05
AFFX-BioDn-5_at 3009.5 P 5.16933e-05
AFFX-CreX-3_at 8953.4 P 4.43055e-05
AFFX-CreX-5_at 7856.5 P 5.16933e-05
AFFX-DapX-3_at 29.314 A 0.425962
AFFX-DapX-5_at 26.072 A 0.262827
AFFX-DapX-M_at 3.6864 A 0.910522
AFFX-LysX-3_at 19.928 A 0.250796
AFFX-LysX-5_at 9.4997 A 0.455412
AFFX-LysX-M_at 9.9273 A 0.960339
AFFX-PheX-3_at 17.032 A 0.960339
AFFX-PheX-5_at 19.707 A 0.5
AFFX-PheX-M_at 5.8446 A 0.883887
AFFX-r2-Bs-dap-3_at 1.7411 A 0.788202
AFFX-r2-Bs-dap-5_at 7.2176 A 0.813028

Total number of rows: 17734

Table truncated, full table size 637 Kbytes.




Supplementary file Size Download File type/resource
GSM320455.CEL.gz 2.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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