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Sample GSM215727 Query DataSets for GSM215727
Status Public on Aug 10, 2007
Title Control (DMSO) treatment rep1
Sample type RNA
 
Source name DMSO treated barley aleurone protoplasts
Organism Hordeum vulgare
Characteristics Protoplasts from Hordeum vulgare L. cv. Himalaya
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from protoplasts in 1:1 (v/v) mixture of TE-saturated phenol and 0.1 M Tris-HCl buffer (pH 8.0) containing 0.1 M LiCl, 10 mM EDTA and 1 % SDS, and precipitated in 2.5 M LiCl according to Shirzadegan et al. (1991) except that extracted samples were not incubated in 80°C. Contaminated DNA was digested with DNase I (Takara, Otsu, Shiga, Japan). mRNA was purified from total RNA using Dynabeads Oligo (dT)25 (DYNAL, Dynal Biotech, Oslo, Norway) after DNase I treatment.
Label biotin
Label protocol 0.3 microgram of mRNA was processed to produce biotinylated cRNA targets.
 
Hybridization protocol Standard Affymetrix procedures
Scan protocol Standard Affymetrix procedures
Description Microarray analysis was performed to know how many gibberellin (GA)-responsive genes are inhibited by beta-Yariv reagent, a specific binder of plant arabinogalactan-proteins
Data processing GCOS
 
Submission date Aug 07, 2007
Last update date Aug 14, 2011
Contact name kiyoshi mashiguchi
Organization name University of Tokyo
Street address 1-1-1 Yayoi, Bunkyo-ku
City Tokyo
ZIP/Postal code 113-8657
Country Japan
 
Platform ID GPL1340
Series (1)
GSE8712 The effects of Yariv-reagent on barley aleurone GA signaling

Data table header descriptions
ID_REF
VALUE GCOS-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
AFFX-BioB-5_at 41.4539 P 0.0032123
AFFX-BioB-M_at 54.7225 P 0.000753643
AFFX-BioB-3_at 43.4822 P 0.000972149
AFFX-BioC-5_at 146.706 P 4.42873e-05
AFFX-BioC-3_at 162.642 P 5.16732e-05
AFFX-BioDn-5_at 474.585 P 4.42873e-05
AFFX-BioDn-3_at 948.267 P 5.16732e-05
AFFX-CreX-5_at 2204.7 P 4.42873e-05
AFFX-CreX-3_at 4462.19 P 4.42873e-05
AFFX-DapX-5_at 0.989827 A 0.659339
AFFX-DapX-M_at 1.69739 A 0.897835
AFFX-DapX-3_at 1.52422 A 0.941556
AFFX-LysX-5_at 0.790209 A 0.834139
AFFX-LysX-M_at 1.1426 A 0.957038
AFFX-LysX-3_at 0.496742 A 0.824693
AFFX-PheX-5_at 1.07127 A 0.891021
AFFX-PheX-M_at 0.764745 A 0.981719
AFFX-PheX-3_at 1.73967 A 0.824672
AFFX-ThrX-5_at 1.24626 A 0.987453
AFFX-ThrX-M_at 1.04969 A 0.749204

Total number of rows: 22840

Table truncated, full table size 795 Kbytes.




Supplementary file Size Download File type/resource
GSM215727.CEL.gz 2.2 Mb (ftp)(http) CEL
GSM215727.CHP.gz 123.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Raw data provided as supplementary file

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