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Sample GSM419979 Query DataSets for GSM419979
Status Public on Sep 16, 2009
Title Awn_Rep2
Sample type RNA
 
Source name Awn
Organism Hordeum vulgare
Characteristics tissue: Awn
Growth protocol Barley plants (Hordeum vulgare L.) cv. Morex were grown in a controlled environment chamber at 22°C/18°C day/night temperatures, 60% RH and a 16 h photoperiod. Plants were grown in 20 cm x 25 cm pots and fertilized using Osmocote® slow release fertilizer.
Extracted molecule total RNA
Extraction protocol RNA from the lemma, the palea and the awn was extracted with guanidinium thiocyanate (Chirgwin et al. 1979). Total RNA from the seed was extracted using Tri Reagent (Molecular Research Center Inc., Cincinnati, OH), followed by precipitation of starch with 0.8 M sodium citrate and 1.2 M NaCl according to the manufacturer’s recommendation.
Label Biotin
Label protocol Biotinylated cRNA was prepared from total RNA according to the the Affymetrix One-Cycle Target Labeling protocol.
 
Hybridization protocol The labeled cRNA was purified and fragmented. Then, hybridization controls were added to the resulting cRNA and hybridized to the Barley1 GeneChips for 16 h at 45°C. Arrays were washed using the GeneChip® Fluidics Station 450.
Scan protocol GenChips were scanned using the GeneChip® 3000 Scanner.
Description This is biological replication 2 for awn collected at the grain-filling stage.
Data processing Cell intensity (CEL) files were imported into Expression Console v 1.1 (Affymetrix) for background correction and normalization using the Microarray Analysis Suite v 5.0 (MAS5) algorithm. Background intensity was corrected as the difference between the perfect match (PM) and mismatch (MM) pair of each probe set. Summarised values were normalized using global scaling. The mean signal of each array was scaled to 500.
 
Submission date Jun 23, 2009
Last update date Sep 16, 2009
Contact name Tilahun Abebe
E-mail(s) Tilahun.Abebe@uni.edu
Phone 319-273-7151
Organization name University of Northern Iowa
Department Biology
Street address 191 McCollum Hall
City Cedar Falls
State/province IA
ZIP/Postal code 50614
Country USA
 
Platform ID GPL1340
Series (1)
GSE16754 Comparative transcriptional profiling of organs of the barley spike

Data table header descriptions
ID_REF
VALUE Log2-transformed MAS5.0 signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 7.714377 P 0.002022599
AFFX-BioB-M_at 7.048796 P 0.000662269
AFFX-BioB-3_at 6.716353 P 0.000146581
AFFX-BioC-5_at 8.957633 P 0.00010954
AFFX-BioC-3_at 8.971751 P 5.17E-05
AFFX-BioDn-5_at 9.680468 P 8.14E-05
AFFX-BioDn-3_at 11.252880 P 0.00010954
AFFX-CreX-5_at 12.206760 P 4.43E-05
AFFX-CreX-3_at 12.864240 P 5.17E-05
AFFX-DapX-5_at 6.933319 P 0.001795911
AFFX-DapX-M_at 7.693933 P 0.000856509
AFFX-DapX-3_at 8.763456 P 0.000296708
AFFX-LysX-5_at 4.098564 A 0.1235723
AFFX-LysX-M_at 5.823424 A 0.2057324
AFFX-LysX-3_at 6.224845 P 0.000195116
AFFX-PheX-5_at 5.199157 P 0.02190186
AFFX-PheX-M_at 5.250981 A 0.2057324
AFFX-PheX-3_at 5.871593 A 0.1089786
AFFX-ThrX-5_at 4.511152 A 0.3544527
AFFX-ThrX-M_at 6.561034 P 0.01138437

Total number of rows: 22840

Table truncated, full table size 821 Kbytes.




Supplementary file Size Download File type/resource
GSM419979.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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