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Sample GSM314275 Query DataSets for GSM314275
Status Public on Aug 11, 2009
Title tissue type: pistil, before anthesis - rep1
Sample type RNA
 
Source name tissue type: pistil, before anthesis
Organism Triticum aestivum
Characteristics PO:0009004## (Organism Part); gametophyte PO:0009004 (Cell type); inflorescence development stages PO:0001083 (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. 2 days before anthesis the central floret was removed from 10 spikes per collection and the pistils were 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. 2 days before anthesis the central floret was removed from 10 spikes per collection and the pistils were frozen in liquid Nitrogen. Development stage: [pistil, 2 days before anthesis]. Sample type: [other::pistil]. 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 453.42 P 7.00908e-05
AFFX-BioB-5_at 421.92 P 0.000662332
AFFX-BioB-M_at 581.85 P 0.000126831
AFFX-BioC-3_at 1952.9 P 4.43055e-05
AFFX-BioC-5_at 1259.2 P 5.16933e-05
AFFX-BioDn-3_at 6704.9 P 7.00908e-05
AFFX-BioDn-5_at 2813.5 P 4.43055e-05
AFFX-CreX-3_at 24390 P 4.43055e-05
AFFX-CreX-5_at 19767 P 5.16933e-05
AFFX-DapX-3_at 3.691 A 0.916408
AFFX-DapX-5_at 13.283 A 0.287743
AFFX-DapX-M_at 25.912 A 0.39692
AFFX-LysX-3_at 21.023 A 0.39692
AFFX-LysX-5_at 23.781 A 0.48511
AFFX-LysX-M_at 8.1047 A 0.67292
AFFX-PheX-3_at 12.269 A 0.794268
AFFX-PheX-5_at 1.101 A 0.987453
AFFX-PheX-M_at 2.3157 A 0.963431
AFFX-r2-Bs-dap-3_at 0.81806 A 0.945245
AFFX-r2-Bs-dap-5_at 4.1755 A 0.703144

Total number of rows: 61290

Table truncated, full table size 2264 Kbytes.




Supplementary file Size Download File type/resource
GSM314275.CEL.gz 8.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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