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Sample GSM320444 Query DataSets for GSM320444
Status Public on Sep 16, 2008
Title protocol: mRNA - genotype: CML69 maize inbred - rep1
Sample type RNA
 
Source name leaf (protocol: mRNA - genotype: CML69 maize inbred)
Organism Zea mays
Characteristics CML69 (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007134 A vegetative growth, PO:0007088 2.04 main shoot and axillary shoots visible at four nodes (Development Stage); 4 week old (Age); Scotts MetroMix 200 (Growth Media).
Growth protocol Growth Description: glasshouse
Extracted molecule total RNA
Extraction protocol Total RNA Isolation in Maize
Label biotin
Label protocol Affymetrix one-cycle target labeling
 
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description Plants grown in glasshouse for 4-weeks (April to May). No supplemental lighting.
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 182.3 P 0.000146616
AFFX-BioB-5_at 145.38 P 0.000972217
AFFX-BioB-M_at 192.97 P 6.0233e-05
AFFX-BioC-3_at 739.75 P 4.43055e-05
AFFX-BioC-5_at 464.87 P 4.43055e-05
AFFX-BioDn-3_at 3594.1 P 5.16933e-05
AFFX-BioDn-5_at 1220.2 P 4.43055e-05
AFFX-CreX-3_at 9194.3 P 4.43055e-05
AFFX-CreX-5_at 6668.3 P 5.16933e-05
AFFX-DapX-3_at 4515.8 P 4.43055e-05
AFFX-DapX-5_at 1965.8 P 4.43055e-05
AFFX-DapX-M_at 3591.3 P 4.43055e-05
AFFX-LysX-3_at 1015.2 P 5.16933e-05
AFFX-LysX-5_at 257.03 P 4.43055e-05
AFFX-LysX-M_at 324.29 P 7.00908e-05
AFFX-PheX-3_at 458.6 P 5.16933e-05
AFFX-PheX-5_at 402.92 P 7.00908e-05
AFFX-PheX-M_at 442.71 P 7.00908e-05
AFFX-r2-Bs-dap-3_at 4528.3 P 0.00167288
AFFX-r2-Bs-dap-5_at 2121.4 P 0.00167288

Total number of rows: 17734

Table truncated, full table size 626 Kbytes.




Supplementary file Size Download File type/resource
GSM320444.CEL.gz 2.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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