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Sample GSM106934 Query DataSets for GSM106934
Status Public on Apr 27, 2006
Title opr3_OPDA_8 hrs_Rep1
Sample type RNA
Source name Stamens
Organism Arabidopsis thaliana
Characteristics A mutation in the gene encoding 12-oxophytodienoic acid reductase (OPR3) results in male sterility in Arabidopsis due to defects in anther development and pollen maturation. Described in Stintzi, A., and Browse, J. (2000). Proc. Natl. Acad. Sci. USA 97, 10625-10630.
Biomaterial provider Browse lab
Treatment protocol Flower buds at developmental stage 12 from opr3 mutants were treated with 0.03% 12-oxophytodienoic acid (OPDA) and stamens were harvested 8 hrs after treatment and immediately frozen in liquid nitrogen
Growth protocol Plants were grown on soil under continuous illumination of 130 mmol m-2s-1 at 22 0C.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from stamens using Trizol reagent following instructions from the manufacturer (Invitrogen Corporation, Carlsbad, CA) and was then purified on RNeasy columns (Qiagen, Valencia, CA).
Label Biotin
Label protocol Labeling and hybridization of RNA was carried out according to standard Affymetrix protocols (Affymetrix, Santa Clara, CA). In brief, ten micrograms of total RNA for each replicate was converted to cDNA, from which biotinylated cRNA target was synthesized. The resulting cRNA was purified on RNeasy columns and then fragmented for hybridization to ATH1 Arabidopsis GeneChips (Affymetrix, Santa Clara, CA).
Hybridization protocol Array was hybridized for 15 hrs, washed and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.
Scan protocol GeneChips were scanned on an Agilent GeneArray Scanner 2500A (Agilent, Palo Alto, CA).
Description Target value (TGT value) was set to 125 global scaling
Data processing Gene chip data files were processed using Affymetrix Microarray Suite MAS 5.0
Submission date Apr 27, 2006
Last update date Aug 28, 2018
Contact name Ajin D Mandaokar
Phone 509-335-2337
Fax 509-335-7643
Organization name Washington State University
Department Institute of Biological Chemistry
Lab Browse lab
Street address 447, Clark hall
City Pullman
State/province WA
ZIP/Postal code 99164-6340
Country USA
Platform ID GPL198
Series (1)
GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
Reanalyzed by GSE118579
Reanalyzed by GSE119083

Data table header descriptions
VALUE Signal intensity calculated after cel file processing by MAS 5.0
ABS_CALL A qualitative measurement indicating if the probe set is detected (Present; P), not detected (Absent; A), or marginally detected (Marginal;M)
DETECTION P-VALUE A p-value indicating the significance of the Detection call

Data table
AFFX-BioB-5_at 115.8 P 0.000509
AFFX-BioB-M_at 177.2 P 0.000081
AFFX-BioB-3_at 124.3 P 0.00011
AFFX-BioC-5_at 310.9 P 0.000127
AFFX-BioC-3_at 173.3 P 0.00007
AFFX-BioDn-5_at 283.4 P 0.000044
AFFX-BioDn-3_at 1279.9 P 0.000052
AFFX-CreX-5_at 3119.5 P 0.000044
AFFX-CreX-3_at 4253.4 P 0.000044
AFFX-DapX-5_at 10.4 A 0.195266
AFFX-DapX-M_at 9.5 A 0.368438
AFFX-DapX-3_at 2.1 A 0.860518
AFFX-LysX-5_at 8.3 A 0.262827
AFFX-LysX-M_at 10.4 A 0.659339
AFFX-LysX-3_at 9.2 A 0.440646
AFFX-PheX-5_at 1.9 A 0.834139
AFFX-PheX-M_at 2.4 A 0.645547
AFFX-PheX-3_at 4 A 0.910522
AFFX-ThrX-5_at 1.4 A 0.921998
AFFX-ThrX-M_at 11.5 A 0.354453

Total number of rows: 22810

Table truncated, full table size 577 Kbytes.

Supplementary file Size Download File type/resource
GSM106934.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM106934.EXP.gz 269 b (ftp)(http) EXP
Raw data provided as supplementary file

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