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Sample GSM825815 Query DataSets for GSM825815
Status Public on Nov 22, 2011
Title genotype: Mla1 - time: 0 - Treated or untreated: Non-inoculated - rep1
Sample type RNA
 
Source name (genotype: Mla1 - time: 0 - Treated or untreated: Non-inoculated)
Organism Hordeum vulgare
Characteristics tissue: leaves
genotype: Mla1
time: 0h
infection: Non-inoculated
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 (organism part); gro: 0007060 (Development Stage); 7 days after planting (Age);
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 Nov 02, 2011
Last update date Nov 22, 2011
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)
GSE33392 Transcription profiling of barley plants containing variants of Mla1 and Mla6 powdery mildew resistance genes

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 77.593 P 0
1289374_Reg_826-1545_at 7.2869 A 0
149174_Reg_66-1115_at 5.9891 A 0
150775_Reg_211-1236_at 50.032 A 0
23381122_R_1101-1898_at 41.884 A 0
2623978_R_1403-2212_at 36.686 A 0
40321-46140.AF427791_x_at 44.566 A 0
48446_Reg_1231-2205_at 4.7781 A 0
48446_Reg_137-1204_at 36.572 A 0
74797-75570.AF427791_x_at 7.748 A 0
8829-9073.AF427791_x_at 28.11 P 0
9507414_R_4264-4644_at 101.42 A 0
A00196.1_at 85.946 A 0
A06498.1_s_at 3.8942 A 0
AB011264_at 16.929 A 0
AB011266_at 49.701 A 0
AB019525_at 34.743 A 0
AB024007_at 26.08 P 0
AF016328_at 90.121 A 0
AF026538_at 113.45 P 0

Total number of rows: 22840

Table truncated, full table size 582 Kbytes.




Supplementary file Size Download File type/resource
GSM825815_0449-30_12563-7_Mla1non0hai-RepI.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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