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Sample GSM314256 Query DataSets for GSM314256
Status Public on Aug 11, 2009
Title tissue type: germinating seed, root - rep3
Sample type RNA
 
Source name tissue type: germinating seed, root
Organism Triticum aestivum
Characteristics PO:0009005## (Organism Part); developing root (Cell type); germination PO:0007057 (Development Stage); 2 days after 2 days after germiniation (Age); 3MM filter paper (Growth Media).
Growth protocol Growth Description: Seeds were germinated in 15 cm petri dishes on damp 3MM filter paper in a growth cabnet set at 22oC light for 16 hrs and 16oC dark for 8 hrs. A single plate containing approximately 50 seeds was sown for each replicate. For each collection for each replicate ten seeds with emerging roots and coleoptile were selected. Roots were excised 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 Seeds were germinated in 15 cm petri dishes on damp 3MM filter paper in a growth cabnet set at 22oC light for 16 hrs and 16oC dark for 8 hrs. A single plate containing approximately 50 seeds was sown for each replicate. For each collection for each replicate ten seeds with emerging roots and coleoptile were selected. Roots were excised and frozen in liquid Nitrogen. Sample type: [germinating 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 287.35 P 5.16933e-05
AFFX-BioB-5_at 337.38 P 0.000753709
AFFX-BioB-M_at 395.89 P 9.45344e-05
AFFX-BioC-3_at 1307.2 P 4.43055e-05
AFFX-BioC-5_at 892.24 P 5.16933e-05
AFFX-BioDn-3_at 5445.2 P 6.0233e-05
AFFX-BioDn-5_at 2072 P 4.43055e-05
AFFX-CreX-3_at 17860 P 4.43055e-05
AFFX-CreX-5_at 13674 P 5.16933e-05
AFFX-DapX-3_at 1455.3 P 5.16933e-05
AFFX-DapX-5_at 410.55 P 5.16933e-05
AFFX-DapX-M_at 967.02 P 0.000258404
AFFX-LysX-3_at 394.08 P 9.45344e-05
AFFX-LysX-5_at 99.248 P 0.000296757
AFFX-LysX-M_at 155.93 P 0.0103167
AFFX-PheX-3_at 265.94 P 0.000340357
AFFX-PheX-5_at 105.11 P 0.0014105
AFFX-PheX-M_at 155.39 P 0.00159264
AFFX-r2-Bs-dap-3_at 2495.9 P 0.00167288
AFFX-r2-Bs-dap-5_at 395.25 P 0.00167288

Total number of rows: 61290

Table truncated, full table size 2260 Kbytes.




Supplementary file Size Download File type/resource
GSM314256.CEL.gz 8.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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