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Sample GSM320449 Query DataSets for GSM320449
Status Public on Sep 16, 2008
Title protocol: Cot filtration (CF) - genotype: B73 maize inbred - rep3
Sample type genomic
 
Source name leaf (protocol: Cot filtration (CF) - genotype: B73 maize inbred)
Organism Zea mays
Characteristics B73 (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 613.86 P 0.00321235
AFFX-BioB-5_at 557.44 P 0.000258404
AFFX-BioB-M_at 793.36 P 0.00159264
AFFX-BioC-3_at 1134.3 P 0.000224712
AFFX-BioC-5_at 1675.9 P 0.000169266
AFFX-BioDn-3_at 4597.5 P 4.43055e-05
AFFX-BioDn-5_at 3271.1 P 5.16933e-05
AFFX-CreX-3_at 10029 P 4.43055e-05
AFFX-CreX-5_at 9137 P 5.16933e-05
AFFX-DapX-3_at 20.028 A 0.58862
AFFX-DapX-5_at 28.893 A 0.275146
AFFX-DapX-M_at 7.8624 A 0.852061
AFFX-LysX-3_at 18.209 A 0.313723
AFFX-LysX-5_at 3.3673 A 0.772364
AFFX-LysX-M_at 9.9655 A 0.852061
AFFX-PheX-3_at 27.823 A 0.804734
AFFX-PheX-5_at 23.463 A 0.544588
AFFX-PheX-M_at 4.9573 A 0.953518
AFFX-r2-Bs-dap-3_at 12.29 A 0.464576
AFFX-r2-Bs-dap-5_at 3.6877 A 0.876244

Total number of rows: 17734

Table truncated, full table size 637 Kbytes.




Supplementary file Size Download File type/resource
GSM320449.CEL.gz 2.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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