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Sample GSM419981 Query DataSets for GSM419981
Status Public on Sep 16, 2009
Title Seed_Rep1
Sample type RNA
 
Source name Seed
Organism Hordeum vulgare
Characteristics tissue: Seed
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 1 for seed 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 7.601275 P 0.001101968
AFFX-BioB-M_at 6.944849 P 0.000445901
AFFX-BioB-3_at 7.099475 P 0.000169227
AFFX-BioC-5_at 8.821621 P 6.02E-05
AFFX-BioC-3_at 9.400370 P 5.17E-05
AFFX-BioDn-5_at 10.182850 P 4.43E-05
AFFX-BioDn-3_at 11.385790 P 8.14E-05
AFFX-CreX-5_at 12.345890 P 4.43E-05
AFFX-CreX-3_at 13.011230 P 4.43E-05
AFFX-DapX-5_at 8.912436 P 6.02E-05
AFFX-DapX-M_at 9.685736 P 0.000195116
AFFX-DapX-3_at 10.697910 P 6.02E-05
AFFX-LysX-5_at 5.848918 P 0.001247504
AFFX-LysX-M_at 7.131546 P 0.0200219
AFFX-LysX-3_at 8.388147 P 0.000126798
AFFX-PheX-5_at 6.916769 P 0.000753643
AFFX-PheX-M_at 6.770703 P 0.001592572
AFFX-PheX-3_at 7.694569 P 0.000169227
AFFX-ThrX-5_at 7.548742 P 0.000258358
AFFX-ThrX-M_at 7.965377 P 0.000146581

Total number of rows: 22840

Table truncated, full table size 820 Kbytes.




Supplementary file Size Download File type/resource
GSM419981.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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