GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM372988 Query DataSets for GSM372988
Status Public on Feb 25, 2009
Title genotype: 11542 - pathogen isolates: 5874 - time: 24 - rep3
Sample type RNA
Source name ##;PO:0009011## (genotype: 11542 - pathogen isolates: 5874 - 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 5874
time: 24, rep-3
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 5874, time 24, 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 at 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
1200459_Reg_88-1740_at 81.239 P 0.00818426
1289374_Reg_826-1545_at 9.2085 A 0.671679
149174_Reg_66-1115_at 22.387 A 0.733153
150775_Reg_211-1236_at 3.6866 A 0.813028
23381122_R_1101-1898_at 121.69 A 0.361054
2623978_R_1403-2212_at 114.15 P 0.0164271
40321-46140.AF427791_x_at 16.671 P 0.02493
48446_Reg_1231-2205_at 38.494 A 0.429432
48446_Reg_137-1204_at 3.5982 A 0.733153
74797-75570.AF427791_x_at 4.78 A 0.761547
8829-9073.AF427791_x_at 1.4835 A 0.60057
9507414_R_4264-4644_at 149.44 A 0.0653326
A00196.1_at 24.576 A 0.570568
A06498.1_s_at 26.599 A 0.535424
AB011264_at 41.11 A 0.211798
AB011266_at 25.165 A 0.296856
AB019525_at 32.102 A 0.535424
AB024007_at 36.752 A 0.238453
AF016328_at 273.95 P 0.0309418
AF026538_at 404.95 P 0.00639609

Total number of rows: 22840

Table truncated, full table size 758 Kbytes.

Supplementary file Size Download File type/resource
GSM372988.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap