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Sample GSM320461 Query DataSets for GSM320461
Status Public on Sep 16, 2008
Title protocol: Methylation filtration (MF) - genotype: Mo17 maize inbred - rep3
Sample type genomic
 
Source name leaf (protocol: Methylation filtration (MF) - 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 Methylation Filtration (MF)
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 1326.6 P 0.00159264
AFFX-BioB-5_at 1156.3 P 0.00010957
AFFX-BioB-M_at 1890.1 P 0.000126831
AFFX-BioC-3_at 2065.7 P 8.1454e-05
AFFX-BioC-5_at 3135.2 P 5.16933e-05
AFFX-BioDn-3_at 9389.4 P 4.43055e-05
AFFX-BioDn-5_at 5714.2 P 5.16933e-05
AFFX-CreX-3_at 18352 P 4.43055e-05
AFFX-CreX-5_at 18378 P 4.43055e-05
AFFX-DapX-3_at 65.938 A 0.5
AFFX-DapX-5_at 25.926 A 0.368438
AFFX-DapX-M_at 7.5 A 0.973889
AFFX-LysX-3_at 5.7085 A 0.724854
AFFX-LysX-5_at 6.2292 A 0.749204
AFFX-LysX-M_at 21.877 A 0.910522
AFFX-PheX-3_at 41.504 A 0.834139
AFFX-PheX-5_at 52.156 A 0.354453
AFFX-PheX-M_at 67.173 A 0.783476
AFFX-r2-Bs-dap-3_at 44.783 P 0.0455804
AFFX-r2-Bs-dap-5_at 32.234 A 0.605162

Total number of rows: 17734

Table truncated, full table size 632 Kbytes.




Supplementary file Size Download File type/resource
GSM320461.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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