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Sample GSM215729 Query DataSets for GSM215729
Status Public on Aug 10, 2007
Title gibberellin plus Yariv-reagent treatment rep1
Sample type RNA
Source name gibberellin plus Yariv-reagent 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
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
AFFX-BioB-5_at 38.9405 P 0.0113844
AFFX-BioB-M_at 26.3872 P 0.000509415
AFFX-BioB-3_at 33.2352 P 0.000258358
AFFX-BioC-5_at 126.21 P 4.42873e-05
AFFX-BioC-3_at 156.967 P 5.16732e-05
AFFX-BioDn-5_at 491.021 P 4.42873e-05
AFFX-BioDn-3_at 897.998 P 4.42873e-05
AFFX-CreX-5_at 2063.9 P 4.42873e-05
AFFX-CreX-3_at 4493.13 P 4.42873e-05
AFFX-DapX-5_at 1.98221 A 0.699394
AFFX-DapX-M_at 1.23197 A 0.921998
AFFX-DapX-3_at 1.2646 A 0.932322
AFFX-LysX-5_at 0.927673 A 0.712257
AFFX-LysX-M_at 1.67976 A 0.897835
AFFX-LysX-3_at 5.94712 A 0.227636
AFFX-PheX-5_at 2.13572 A 0.814869
AFFX-PheX-M_at 7.30829 A 0.470238
AFFX-PheX-3_at 6.88616 A 0.250796
AFFX-ThrX-5_at 0.71563 A 0.978098
AFFX-ThrX-M_at 9.61611 A 0.156732

Total number of rows: 22840

Table truncated, full table size 795 Kbytes.

Supplementary file Size Download File type/resource
GSM215729.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM215729.CHP.gz 123.7 Kb (ftp)(http) CHP
Processed data included within Sample table

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