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Sample GSM320471 Query DataSets for GSM320471
Status Public on Sep 16, 2008
Title protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred - rep1
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 13880 P 0.00179598
AFFX-BioB-5_at 13535 P 4.43055e-05
AFFX-BioB-M_at 17111 P 0.00110204
AFFX-BioC-3_at 24085 P 4.43055e-05
AFFX-BioC-5_at 38220 P 4.43055e-05
AFFX-BioDn-3_at 122930 P 4.43055e-05
AFFX-BioDn-5_at 72021 P 0.000126831
AFFX-CreX-3_at 214240 P 4.43055e-05
AFFX-CreX-5_at 210980 P 4.43055e-05
AFFX-DapX-3_at 115.18 A 0.891021
AFFX-DapX-5_at 310.42 A 0.354453
AFFX-DapX-M_at 116.6 A 0.834139
AFFX-LysX-3_at 128.1 A 0.60308
AFFX-LysX-5_at 388.26 A 0.287743
AFFX-LysX-M_at 81.803 A 0.921998
AFFX-PheX-3_at 572.54 A 0.712257
AFFX-PheX-5_at 190.81 A 0.699394
AFFX-PheX-M_at 151.91 A 0.794268
AFFX-r2-Bs-dap-3_at 119.09 A 0.361054
AFFX-r2-Bs-dap-5_at 135.82 A 0.733153

Total number of rows: 17734

Table truncated, full table size 603 Kbytes.




Supplementary file Size Download File type/resource
GSM320471.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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