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Sample GSM215730 Query DataSets for GSM215730
Status Public on Aug 10, 2007
Title Control (DMSO) treatment rep2
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 24.3529 P 0.0284573
AFFX-BioB-M_at 29.362 P 9.4506e-05
AFFX-BioB-3_at 26.8082 P 0.0020226
AFFX-BioC-5_at 100.3 P 4.42873e-05
AFFX-BioC-3_at 134.166 P 7.00668e-05
AFFX-BioDn-5_at 359.717 P 4.42873e-05
AFFX-BioDn-3_at 672.622 P 4.42873e-05
AFFX-CreX-5_at 1520.74 P 4.42873e-05
AFFX-CreX-3_at 3924.46 P 4.42873e-05
AFFX-DapX-5_at 6.31655 A 0.123572
AFFX-DapX-M_at 1.06579 A 0.868639
AFFX-DapX-3_at 1.32692 A 0.916408
AFFX-LysX-5_at 0.725613 A 0.824672
AFFX-LysX-M_at 0.951239 A 0.852061
AFFX-LysX-3_at 0.86009 A 0.659339
AFFX-PheX-5_at 1.17375 A 0.9273
AFFX-PheX-M_at 0.883045 A 0.843268
AFFX-PheX-3_at 2.28629 A 0.794268
AFFX-ThrX-5_at 0.876875 A 0.941556
AFFX-ThrX-M_at 4.23317 A 0.645547

Total number of rows: 22840

Table truncated, full table size 795 Kbytes.




Supplementary file Size Download File type/resource
GSM215730.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM215730.CHP.gz 123.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Raw data provided as supplementary file

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