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Sample GSM281747 Query DataSets for GSM281747
Status Public on May 27, 2008
Title Genotype: Steptoe - rep3
Sample type RNA
Source name leaf (genotype: Steptoe)
Organism Hordeum vulgare
Characteristics cultivar Steptoe (Germplasm Name); PO:0009025 leaf, (Organism Part); GRO:0007060 (Development Stage); 7 days (Age); garden soil (Growth Media).
Growth protocol Growth Description: Seedlings were grown in the greenhouse for 7 days. No supplemental lighting was used.
Extracted molecule total RNA
Extraction protocol Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up
Label biotin
Label protocol Affy-Eukaryotic Target Preparation
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description Steptoe, 7 day old seedling (first leaf unfolded), rep 3
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. The normalization scripts are available from the PLEXdb team by request.
Submission date Apr 15, 2008
Last update date May 27, 2008
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 GPL1340
Series (1)
GSE11182 Steptoe x Morex seedling leaf comparison

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
1200459_Reg_88-1740_at 8.7328 A 0.5
1289374_Reg_826-1545_at 3.9515 A 0.703144
149174_Reg_66-1115_at 14.359 A 0.835968
150775_Reg_211-1236_at 3.6476 A 0.788202
23381122_R_1101-1898_at 106.1 A 0.143002
2623978_R_1403-2212_at 46.649 A 0.553048
40321-46140.AF427791_x_at 23.284 A 0.318935
48446_Reg_1231-2205_at 6.6723 A 0.97957
48446_Reg_137-1204_at 9.5143 A 0.703144
74797-75570.AF427791_x_at 54.955 A 0.164032
8829-9073.AF427791_x_at 39.817 A 0.0844035
9507414_R_4264-4644_at 140.21 A 0.429432
A00196.1_at 64.361 A 0.429432
A06498.1_s_at 10.457 A 0.835968
AB011264_at 32.498 A 0.143002
AB011266_at 66.917 A 0.123873
AB019525_at 13.412 A 0.570568
AB024007_at 17.617 A 0.296856
AF016328_at 68.754 A 0.429432
AF026538_at 135.18 A 0.123873

Total number of rows: 22840

Table truncated, full table size 757 Kbytes.

Supplementary file Size Download File type/resource
GSM281747.CEL.gz 3.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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