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Sample GSM440958 Query DataSets for GSM440958
Status Public on Sep 30, 2009
Title Control lemma_Rep2
Sample type RNA
 
Source name Well-watered barley plants
Organism Hordeum vulgare
Characteristics organ: Lemma
treatment: Control
Treatment protocol Drought stress was initiated at Zadok stage 71 (kernel watery-ripe; Zadoks et al., 1974) by withholding water for 4 days. Non-stressed (control) plants received 500 ml water every day.
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, palea and 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 Gene expression data from well-watered lemma
Data processing Cell intensity (CEL) files were imported into Expression Console v 1.1 (Affymetrix) for background correction, normalization and summarization 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 Aug 17, 2009
Last update date Sep 30, 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)
GSE17669 Gene expression in the barley spike during drought stress

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 7.700569 P 0.004017214
AFFX-BioB-M_at 6.738111 P 0.000258358
AFFX-BioB-3_at 6.54583 P 0.000296708
AFFX-BioC-5_at 8.757848 P 6.02E-05
AFFX-BioC-3_at 8.791629 P 5.17E-05
AFFX-BioDn-5_at 9.602208 P 7.01E-05
AFFX-BioDn-3_at 11.01221 P 9.45E-05
AFFX-CreX-5_at 11.89425 P 4.43E-05
AFFX-CreX-3_at 12.60973 P 4.43E-05
AFFX-DapX-5_at 6.407482 P 0.004017214
AFFX-DapX-M_at 7.654875 P 0.000856509
AFFX-DapX-3_at 8.403939 P 9.45E-05
AFFX-LysX-5_at 4.296365 A 0.1658614
AFFX-LysX-M_at 5.538715 A 0.1851306
AFFX-LysX-3_at 5.502285 P 0.001101968
AFFX-PheX-5_at 3.571137 A 0.313723
AFFX-PheX-M_at 2.4803 A 0.6030805
AFFX-PheX-3_at 5.597758 A 0.07800179
AFFX-ThrX-5_at 5.068757 A 0.1479388
AFFX-ThrX-M_at 5.871553 P 0.0200219

Total number of rows: 22840

Table truncated, full table size 819 Kbytes.




Supplementary file Size Download File type/resource
GSM440958.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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