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Sample GSM314281 Query DataSets for GSM314281
Status Public on Aug 11, 2009
Title tissue type: 3-5 DAP caryopsis - rep1
Sample type RNA
 
Source name tissue type: 3-5 DAP caryopsis
Organism Triticum aestivum
Characteristics PO:0009010## (Organism Part); seed PO:0009010 (Cell type); seed development stages PO:0001170 (Development Stage); 1 after planting (Age); Cereal mix (Growth Media).
Growth protocol Growth Description: 20 cm pots were sown with 2 seeds at a depth of 2 cm. 14 days after germination the weaker seedling was removed. Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC. 3-5 days after pollination the central floret was removed from 10 spikes per collection and the caryopsis was frozen in liquid Nitrogen.
Extracted molecule total RNA
Extraction protocol RNA Isolation Using Trizol And Qiagen RNAeasy Columns
Label biotin
Label protocol Affy-Eukaryotic Target Preparation
 
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description 20 cm pots were sown with 2 seeds at a depth of 2 cm. 14 days after germination the weaker seedling was removed. Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC. 3-5 days after pollination the central floret was removed from 10 spikes per collection and the caryopsis was frozen in liquid Nitrogen. Development stage: [caryopsis, 3-5 DAP]. Sample type: [ developing seed]. Individual genetic trait genotype: [Chinese Spring]. Treatment application type: [No Treatment].
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 Aug 20, 2008
Last update date Aug 11, 2009
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 GPL3802
Series (1)
GSE12508 Transcription patterns during wheat development

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 399.89 P 5.16933e-05
AFFX-BioB-5_at 391.92 P 0.000195157
AFFX-BioB-M_at 525.33 P 5.16933e-05
AFFX-BioC-3_at 1716.7 P 4.43055e-05
AFFX-BioC-5_at 1212.4 P 4.43055e-05
AFFX-BioDn-3_at 7060.6 P 4.43055e-05
AFFX-BioDn-5_at 2675 P 4.43055e-05
AFFX-CreX-3_at 19995 P 4.43055e-05
AFFX-CreX-5_at 15802 P 5.16933e-05
AFFX-DapX-3_at 3183.5 P 4.43055e-05
AFFX-DapX-5_at 427 P 5.16933e-05
AFFX-DapX-M_at 1580.4 P 8.1454e-05
AFFX-LysX-3_at 916.78 P 4.43055e-05
AFFX-LysX-5_at 195.29 P 5.16933e-05
AFFX-LysX-M_at 259 P 0.000856576
AFFX-PheX-3_at 520.63 P 4.43055e-05
AFFX-PheX-5_at 217.58 P 0.00010957
AFFX-PheX-M_at 251.51 P 0.000126831
AFFX-r2-Bs-dap-3_at 4501.8 P 0.00167288
AFFX-r2-Bs-dap-5_at 405.13 P 0.00167288

Total number of rows: 61290

Table truncated, full table size 2263 Kbytes.




Supplementary file Size Download File type/resource
GSM314281.CEL.gz 8.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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