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Sample GSM431546 Query DataSets for GSM431546
Status Public on Jul 24, 2009
Title pathogen isolates: Mock - rep1
Sample type RNA
 
Source name root (pathogen isolates: Mock)
Organism Hordeum vulgare
Characteristics cultivar: Regina
tissue: root
Extracted molecule total RNA
Extraction protocol Trizol total RNA extraction, Qiagen RNeasy column purification
Label biotin
Label protocol Affy-Eukaryotic Target Preparation
 
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description regina (germplasm name); po: 0009005 root, (Organism Part); PO:0007520 root development stages (Development Stage); sand (Growth Media).
Four day old barley cv. Regina roots inoculated with zoospore-free buffer (0.1 g L-1 Phostrogen, 0.5% Bovine serum albumen) as mock inoculation control. Sample prepared for roots collected from ten seedlings from each of the ten time points (15’, 30’, 45’ 1h, 2h, 3h, 4h, 5h, 6h, 7h) were combined for each treatment to give a time course pool. RNA was extracted from this time course pool and used for subsequent experiments.
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 Jul 21, 2009
Last update date Jul 23, 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 GPL1340
Series (1)
GSE17238 Response of barley roots during the host interaction with the plasmodiophorid virus vector Polymyxa graminis

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
1200459_Reg_88-1740_at 69.067 P 0
1289374_Reg_826-1545_at 8.9892 A 0
149174_Reg_66-1115_at 14.709 A 0
150775_Reg_211-1236_at 3.8309 A 0
23381122_R_1101-1898_at 109.02 A 0
2623978_R_1403-2212_at 56.764 P 0
40321-46140.AF427791_x_at 9.9335 A 0
48446_Reg_1231-2205_at 38.318 A 0
48446_Reg_137-1204_at 2.9118 A 0
74797-75570.AF427791_x_at 11.156 A 0
8829-9073.AF427791_x_at 12.588 A 0
9507414_R_4264-4644_at 143.49 M 0
A00196.1_at 30.791 A 0
A06498.1_s_at 5.0537 A 0
AB011264_at 26.361 A 0
AB011266_at 47.661 A 0
AB019525_at 22.332 A 0
AB024007_at 7.9787 A 0
AF016328_at 195 A 0
AF026538_at 911.87 P 0

Total number of rows: 22840

Table truncated, full table size 582 Kbytes.




Supplementary file Size Download File type/resource
GSM431546_Mock_rep1.CEL.gz 2.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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