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Sample GSM315203 Query DataSets for GSM315203
Status Public on Jun 11, 2009
Title target strand labeled: Antisense - rep1
Sample type other
Source name whole plant (target strand labeled: Antisense)
Organism Triticum aestivum
Characteristics Chinese Spring (Germplasm Name); PO:0000003 whole plant, (Organism Part); PO:0007033 whole plant growth stages (Development Stage); peat/perlite/soil (Growth Media).
Growth protocol Growth Description: For each tissue type except ‘Germinated seed’, six seeds were planted in 6-inch round pots using a potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate). Seedlings were grown to the appropriate growth stages for tissue collection in a greenhouse with a stable temperature of 25±2ºC and a 16 h light/8 h dark cycle.
Extracted molecule other
Extraction protocol Trizol Plus RNA Purification (Invitrogen)
Label biotin
Label protocol Affy- Whole transcript target preparation
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description Mixed RNA form 5 tissue types of Chinese Spring wheat cultivar. Tissue types were; i.Germinated seed (germinated on wetted filter paper in a petri-dish in the dark for two days), ii.Shoot (Feekes 1.2, emergence with second leaf unfolded), iii.Flag leaf (Feekes 9.0, flag leaf stage with ligule emerged), iv.Spike pre-anthesis (Feekes 10.5, heading complete), and v.Spike post-anthesis (Feekes 10.5.3, flowering complete to base of spike).
Data processing The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor ( 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 The normalization scripts are available from the PLEXdb team by request.
Submission date Aug 22, 2008
Last update date Jun 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)
GSE12528 Wheat "Chinese Spring" natural antisense transcription survey

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
AFFX-BioB-3_at 63626 P 0
AFFX-BioB-5_at 37298 P 0
AFFX-BioB-M_at 89616 P 0
AFFX-BioC-3_at 120930 P 0
AFFX-BioC-5_at 126950 P 0
AFFX-BioDn-3_at 321210 P 0
AFFX-BioDn-5_at 250640 P 0
AFFX-CreX-3_at 800130 P 0
AFFX-CreX-5_at 802400 P 0
AFFX-DapX-3_at 1955.6 P 0
AFFX-DapX-5_at 4205.4 P 0
AFFX-DapX-M_at 3060.2 P 0
AFFX-LysX-3_at 74.481 A 0
AFFX-LysX-5_at 551.29 A 0
AFFX-LysX-M_at 77.637 A 0
AFFX-PheX-3_at 203.7 A 0
AFFX-PheX-5_at 1558.6 P 0
AFFX-PheX-M_at 450.94 A 0
AFFX-r2-Bs-dap-3_at 1349.4 P 0
AFFX-r2-Bs-dap-5_at 5785.1 P 0

Total number of rows: 61290

Table truncated, full table size 1800 Kbytes.

Supplementary file Size Download File type/resource
GSM315203.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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