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Sample GSM106912 Query DataSets for GSM106912
Status Public on Apr 27, 2006
Title opr3_JA 8hrs_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% methyl jasmonate 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
E-mail(s) ajin@mail.wsu.edu
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
Relations
Reanalyzed by GSE118579
Reanalyzed by GSE119083

Data table header descriptions
ID_REF
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
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 164.3 P 0.000662
AFFX-BioB-M_at 204 P 0.00006
AFFX-BioB-3_at 140.3 P 0.000052
AFFX-BioC-5_at 342.4 P 0.000127
AFFX-BioC-3_at 160.4 P 0.000081
AFFX-BioDn-5_at 314.5 P 0.000044
AFFX-BioDn-3_at 1300.6 P 0.000052
AFFX-CreX-5_at 3437.3 P 0.000044
AFFX-CreX-3_at 4256.4 P 0.000044
AFFX-DapX-5_at 11.1 A 0.250796
AFFX-DapX-M_at 8.8 A 0.340661
AFFX-DapX-3_at 1.9 A 0.737173
AFFX-LysX-5_at 5.1 A 0.559354
AFFX-LysX-M_at 20.5 A 0.5
AFFX-LysX-3_at 2.2 A 0.262827
AFFX-PheX-5_at 1.7 A 0.794268
AFFX-PheX-M_at 3.7 A 0.617401
AFFX-PheX-3_at 4.2 A 0.672921
AFFX-ThrX-5_at 4.2 A 0.659339
AFFX-ThrX-M_at 6.1 A 0.5

Total number of rows: 22810

Table truncated, full table size 577 Kbytes.




Supplementary file Size Download File type/resource
GSM106912.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM106912.EXP.gz 491 b (ftp)(http) EXP
Raw data provided as supplementary file

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