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Sample GSM431573 Query DataSets for GSM431573
Status Public on Jul 24, 2009
Title pathogen isolates: Polymyxa betae - rep3
Sample type RNA
 
Source name root (pathogen isolates: Polymyxa betae)
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 were inoculated with a zoospore suspension of 1 x 10 6 spores mL-1 P. betae in buffer (0.1 g L-1 Phostrogen, 0.5% Bovine serum albumen). 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)
GSE17240 Response of barley roots during the non-host interaction with the plasmodiophorid virus vector Polymyxa betae

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 49.628 A 0
1289374_Reg_826-1545_at 4.0071 A 0
149174_Reg_66-1115_at 10.835 A 0
150775_Reg_211-1236_at 16.278 A 0
23381122_R_1101-1898_at 89.112 A 0
2623978_R_1403-2212_at 12.029 A 0
40321-46140.AF427791_x_at 12.347 A 0
48446_Reg_1231-2205_at 8.3412 A 0
48446_Reg_137-1204_at 1.4587 A 0
74797-75570.AF427791_x_at 10.039 A 0
8829-9073.AF427791_x_at 29.018 A 0
9507414_R_4264-4644_at 95.773 A 0
A00196.1_at 36.526 A 0
A06498.1_s_at 6.5439 A 0
AB011264_at 4.0333 A 0
AB011266_at 19.225 A 0
AB019525_at 30.384 A 0
AB024007_at 4.2329 A 0
AF016328_at 169.2 A 0
AF026538_at 607.95 P 0

Total number of rows: 22840

Table truncated, full table size 582 Kbytes.




Supplementary file Size Download File type/resource
GSM431573_Nonhost_rep3.CEL.gz 1.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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