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Sample GSM320457 Query DataSets for GSM320457
Status Public on Sep 16, 2008
Title protocol: Methylation filtration (MF) - genotype: B73 maize inbred - rep2
Sample type genomic
 
Source name leaf (protocol: Methylation filtration (MF) - 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 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 1588.4 P 0.000445958
AFFX-BioB-5_at 1582 P 8.1454e-05
AFFX-BioB-M_at 1798.2 P 0.000224712
AFFX-BioC-3_at 2250.4 P 5.16933e-05
AFFX-BioC-5_at 3001.5 P 4.43055e-05
AFFX-BioDn-3_at 10165 P 4.43055e-05
AFFX-BioDn-5_at 6260.1 P 7.00908e-05
AFFX-CreX-3_at 18094 P 4.43055e-05
AFFX-CreX-5_at 16922 P 4.43055e-05
AFFX-DapX-3_at 105.27 A 0.354453
AFFX-DapX-5_at 80.813 A 0.195266
AFFX-DapX-M_at 13.131 A 0.921998
AFFX-LysX-3_at 35.619 A 0.313723
AFFX-LysX-5_at 44.54 A 0.354453
AFFX-LysX-M_at 11.688 A 0.988616
AFFX-PheX-3_at 31.594 A 0.9273
AFFX-PheX-5_at 59.35 A 0.0894781
AFFX-PheX-M_at 9.1144 A 0.891021
AFFX-r2-Bs-dap-3_at 17.196 A 0.361054
AFFX-r2-Bs-dap-5_at 12.237 A 0.876127

Total number of rows: 17734

Table truncated, full table size 633 Kbytes.




Supplementary file Size Download File type/resource
GSM320457.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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