NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM314263 Query DataSets for GSM314263
Status Public on Aug 11, 2009
Title tissue type: seedling, crown - rep1
Sample type RNA
 
Source name tissue type: seedling, crown
Organism Triticum aestivum
Characteristics PO:0009006## (Organism Part); shoot PO:0009006 (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. The crown from 10 plants per collection was 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 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. The crown from 10 plants per collection was excised and frozen in liquid Nitrogen. Development stage: [10 cm seedling]. Sample type: [crown]. 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 201.6 P 7.00908e-05
AFFX-BioB-5_at 293.08 P 0.00124757
AFFX-BioB-M_at 273.22 P 7.00908e-05
AFFX-BioC-3_at 929.43 P 4.43055e-05
AFFX-BioC-5_at 648.35 P 7.00908e-05
AFFX-BioDn-3_at 4556.1 P 7.00908e-05
AFFX-BioDn-5_at 1475.7 P 5.16933e-05
AFFX-CreX-3_at 15176 P 4.43055e-05
AFFX-CreX-5_at 11329 P 5.16933e-05
AFFX-DapX-3_at 1205.3 P 6.0233e-05
AFFX-DapX-5_at 235.28 P 6.0233e-05
AFFX-DapX-M_at 798.84 P 0.000662332
AFFX-LysX-3_at 383.73 P 7.00908e-05
AFFX-LysX-5_at 98.467 P 0.000126831
AFFX-LysX-M_at 115.29 A 0.0780018
AFFX-PheX-3_at 161.51 P 0.00179598
AFFX-PheX-5_at 97.299 P 0.0125467
AFFX-PheX-M_at 84.714 P 0.00321235
AFFX-r2-Bs-dap-3_at 2110.3 P 0.00167288
AFFX-r2-Bs-dap-5_at 244.83 P 0.00167288

Total number of rows: 61290

Table truncated, full table size 2265 Kbytes.




Supplementary file Size Download File type/resource
GSM314263.CEL.gz 8.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap