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Sample GSM314260 Query DataSets for GSM314260
Status Public on Aug 11, 2009
Title tissue type: seedling, root - rep1
Sample type RNA
 
Source name tissue type: seedling, root
Organism Triticum aestivum
Characteristics PO:0009005## (Organism Part); root PO:0009005 (Cell type); vegetative growth PO:0007134 (Development Stage); 10 days after planting (Age); vermiculite (Growth Media).
Growth protocol Growth Description: Three seeds were planted in a single 10 cm pot containing vermiculite. 20 pots were sown for each replicate. When seedlings reached 10 cm (9-11 cm above surface of vermiculite) they were sampled randomly and vermiculite was removed by washing in RO water. Roots from 10 plants per collection were excised at the base and 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 Three seeds were planted in a single 10 cm pot containing vermiculite. 20 pots were sown for each replicate. When seedlings reached 10 cm (9-11 cm above surface of vermiculite) they were sampled randomly and vermiculite was removed by washing in RO water. Roots from 10 plants per collection were excised at the base and frozen in liquid Nitrogen. Development stage: [10 cm seedling]. Sample type: [root]. 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 438.17 P 8.1454e-05
AFFX-BioB-5_at 420.8 P 0.000753709
AFFX-BioB-M_at 551.6 P 9.45344e-05
AFFX-BioC-3_at 1779.6 P 4.43055e-05
AFFX-BioC-5_at 1298.9 P 4.43055e-05
AFFX-BioDn-3_at 7033.3 P 6.0233e-05
AFFX-BioDn-5_at 2377.4 P 4.43055e-05
AFFX-CreX-3_at 21743 P 4.43055e-05
AFFX-CreX-5_at 16600 P 5.16933e-05
AFFX-DapX-3_at 5.0669 A 0.794268
AFFX-DapX-5_at 16.461 A 0.156732
AFFX-DapX-M_at 8.6768 A 0.425962
AFFX-LysX-3_at 26.052 M 0.0542134
AFFX-LysX-5_at 7.7391 A 0.39692
AFFX-LysX-M_at 4.897 A 0.937071
AFFX-PheX-3_at 50.382 A 0.32708
AFFX-PheX-5_at 3.1809 A 0.9273
AFFX-PheX-M_at 2.3408 A 0.932322
AFFX-r2-Bs-dap-3_at 0.88393 A 0.893388
AFFX-r2-Bs-dap-5_at 24.693 A 0.186972

Total number of rows: 61290

Table truncated, full table size 2264 Kbytes.




Supplementary file Size Download File type/resource
GSM314260.CEL.gz 8.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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