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Sample GSM320445 Query DataSets for GSM320445
Status Public on Sep 16, 2008
Title protocol: mRNA - genotype: CML69 maize inbred - rep2
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 143.72 P 4.43055e-05
AFFX-BioB-5_at 117.45 P 0.000509474
AFFX-BioB-M_at 152.48 P 5.16933e-05
AFFX-BioC-3_at 634.23 P 4.43055e-05
AFFX-BioC-5_at 419.12 P 4.43055e-05
AFFX-BioDn-3_at 2295.9 P 5.16933e-05
AFFX-BioDn-5_at 1102.5 P 4.43055e-05
AFFX-CreX-3_at 7431.5 P 4.43055e-05
AFFX-CreX-5_at 5407.5 P 5.16933e-05
AFFX-DapX-3_at 3920.1 P 4.43055e-05
AFFX-DapX-5_at 1704.9 P 4.43055e-05
AFFX-DapX-M_at 3147.9 P 4.43055e-05
AFFX-LysX-3_at 719.39 P 4.43055e-05
AFFX-LysX-5_at 247.36 P 4.43055e-05
AFFX-LysX-M_at 312.94 P 5.16933e-05
AFFX-PheX-3_at 379.09 P 4.43055e-05
AFFX-PheX-5_at 376.92 P 5.16933e-05
AFFX-PheX-M_at 443.75 P 4.43055e-05
AFFX-r2-Bs-dap-3_at 3624.2 P 0.00167288
AFFX-r2-Bs-dap-5_at 1933.4 P 0.00167288

Total number of rows: 17734

Table truncated, full table size 627 Kbytes.




Supplementary file Size Download File type/resource
GSM320445.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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