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Sample GSM826227 Query DataSets for GSM826227
Status Public on Nov 22, 2011
Title treated or untreated: water control - time: 24 hrs - rep2
Sample type RNA
 
Source name leaf (treated or untreated: water control - time: 24 hrs)
Organism Hordeum vulgare
Characteristics tissue: leaf
time: 24 hrs
infection: water control
Growth protocol Growth Description: Growth chamber grown Environmental Conditions: Seeds were stored at 4 deg C for one week. Plants were then moved to a growth chamber set to 20-22 deg C, approx. 70% RH, with 14hr photoperiod provided by 160 W VHO fluorescent and 60 W incandescent lamps. Plants were watered daily or as needed.
Extracted molecule total RNA
Extraction protocol RNA Isolation Using Trizol And Qiagen RNAeasy Columns
Label biotin
Label protocol Affymetrix one-cycle target labeling
 
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description hv ssp spontaneum accession shechem 12-32 (germplasm name); po: 0009025 leaf, (Organism Part); PO:0001052 2 leaf expansion stage (Development Stage); 2 weeks (Age); 50% steamed soil, 50% Metro Mix 200 (Growth Media).
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)
GSE33401 Transcriptome analysis of wild barley (H. vulgare ssp spontaneum) after pathogen inoculation

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 40.6 P 0
1289374_Reg_826-1545_at 5.1398 A 0
149174_Reg_66-1115_at 4.3208 A 0
150775_Reg_211-1236_at 15.593 A 0
23381122_R_1101-1898_at 55.99 A 0
2623978_R_1403-2212_at 35.828 A 0
40321-46140.AF427791_x_at 12.473 P 0
48446_Reg_1231-2205_at 3.2686 A 0
48446_Reg_137-1204_at 1.139 A 0
74797-75570.AF427791_x_at 5.7779 A 0
8829-9073.AF427791_x_at 6.2439 A 0
9507414_R_4264-4644_at 107.66 A 0
A00196.1_at 16.504 A 0
A06498.1_s_at 3.7192 A 0
AB011264_at 24.69 P 0
AB011266_at 20.296 A 0
AB019525_at 6.7716 A 0
AB024007_at 9.9714 A 0
AF016328_at 59.106 A 0
AF026538_at 175.06 P 0

Total number of rows: 22840

Table truncated, full table size 582 Kbytes.




Supplementary file Size Download File type/resource
GSM826227_Water_24hai_18.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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