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Sample GSM373004 Query DataSets for GSM373004
Status Public on Feb 25, 2009
Title genotype: 11542 - pathogen isolates: K1 - time: 24 - rep1
Sample type RNA
 
Source name ##;PO:0009011## (genotype: 11542 - pathogen isolates: K1 - time: 24)
Organism Hordeum vulgare
Characteristics germplasm name: c.i. 16151-m11542
organism part: PO:0009011
seedling growth: GRO:0007058
development stage: first leaf unfolded GRO:0007060
age: 7 days after sowing
growth media: peat/perlite/soil
genotype: bcd1 mutant, pathogen isolate K1
time: 24, rep-1
Growth protocol Growth Description: GH grown and inoculated in 18oC chamber
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 bcd1 mutant, pathogen isolate K1, time 24, rep-1
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 Feb 20, 2009
Last update date Feb 24, 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)
GSE14930 Comparison of wild-type and cell death mutant of barley plants containing Mla6 powdery mildew resistance gene

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 64.471 A 0.0911573
1289374_Reg_826-1545_at 14.706 A 0.429432
149174_Reg_66-1115_at 28.333 A 0.703144
150775_Reg_211-1236_at 7.6231 A 0.605162
23381122_R_1101-1898_at 170.47 A 0.211798
2623978_R_1403-2212_at 81.667 P 0.0252302
40321-46140.AF427791_x_at 8.8132 P 0.00382459
48446_Reg_1231-2205_at 58.821 A 0.464576
48446_Reg_137-1204_at 3.5179 A 0.788202
74797-75570.AF427791_x_at 3.2722 A 0.733153
8829-9073.AF427791_x_at 17.782 A 0.439241
9507414_R_4264-4644_at 226.57 A 0.123873
A00196.1_at 17.231 A 0.638946
A06498.1_s_at 10.037 A 0.638946
AB011264_at 27.965 A 0.186972
AB011266_at 59.464 A 0.186972
AB019525_at 27.605 A 0.464576
AB024007_at 21.464 A 0.464576
AF016328_at 184.49 A 0.0653326
AF026538_at 246.22 P 0.0164271

Total number of rows: 22840

Table truncated, full table size 760 Kbytes.




Supplementary file Size Download File type/resource
GSM373004.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

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