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Sample GSM363461 Query DataSets for GSM363461
Status Public on Jan 24, 2009
Title Control (C) - rep2
Sample type RNA
 
Source name leaf: Control (C)
Organism Hordeum vulgare
Characteristics cultivar Hamidiye (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007098 LP.02 two leaves visible (Development Stage); 13 days old (Age); hydroponic 1/2 strength hoagland's solution (Growth Media).
Growth protocol Growth Description: Aseptical germination and growth on half strength Hoagland’s solution (Hoagland and Arnon, 1950) (pH 5.8) solidified with Phytagel® for 8 days and transfer to sterile hydroponic half strength Hoagland’s solution containing 10 micromolar boric acid (B(OH)3) (control) Environmental Conditions: 23±2ºC, 16 h light (400 µmol m–2 s–1) and 8 h dark photo-cycle, 70% relative humidity
Extracted molecule total RNA
Extraction protocol TRIzol Reagent (Qiagen) and sodium acetate-ethanol precipitation
Label biotin
Label protocol Affy-Eukaryotic Target Preparation
 
Hybridization protocol Affy- Eukaryotic Target Hybridization
Scan protocol Affy- Array Scanning
Description Eight day old aseptically grown seedlings were subjected to 10 uM (micromolar) boric acid (B(OH)3) treatment (control) for 5 days and expression profiles were determined with DNA microarrays using total RNA from leaf tissues
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 Jan 22, 2009
Last update date Jan 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)
GSE14521 Late response to boron toxicity in barley leaves

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)

Data table
ID_REF VALUE ABS_CALL
1200459_Reg_88-1740_at 31.591 A
1289374_Reg_826-1545_at 2.8297 A
149174_Reg_66-1115_at 32.551 A
150775_Reg_211-1236_at 10.788 A
23381122_R_1101-1898_at 11.137 A
2623978_R_1403-2212_at 20.407 P
40321-46140.AF427791_x_at 5.117 A
48446_Reg_1231-2205_at 4.6662 A
48446_Reg_137-1204_at 1.6111 A
74797-75570.AF427791_x_at 4.4673 A
8829-9073.AF427791_x_at 8.0388 A
9507414_R_4264-4644_at 49.922 A
A00196.1_at 12.767 A
A06498.1_s_at 2.5638 A
AB011264_at 27.326 A
AB011266_at 16.585 A
AB019525_at 3.1491 A
AB024007_at 15.126 A
AF016328_at 65.049 A
AF026538_at 142.13 P

Total number of rows: 22840

Table truncated, full table size 537 Kbytes.




Supplementary file Size Download File type/resource
GSM363461.CEL.gz 2.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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