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Sample GSM617573 Query DataSets for GSM617573
Status Public on Dec 31, 2010
Title bzr1-1Dxbri1-116, rep 2
Sample type RNA
 
Source name Homozygote bzr1-1D;bri1-116
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia
genotype/variation: bzr1-1D;bri1-116 double mutant
tissue: seedling
Treatment protocol The seedlings were frozen in liquid nitrogen in complete darkness and then the homozygote seedlings of bri1-116 were picked individually from the heterozygous population.
Growth protocol Homozygote bzr1-1D;bri1-116, segregating bri1-116, and wild type Col were grown on solid ½ MS medium with 1% sucrose in the dark for 108 hours.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by Plant RNA Purification Reagent (Invitrogen), treated with RNase-free DNase I (Qiagen), and cleaned up using RNeasy Plant Mini column (Qiagen) according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared from 10ug of total RNA according to the Eukaryotic Target Protocol (Affymetrix).
 
Hybridization protocol 20 μg of labeled and fragmented cRNA were hybridized with Arabidopsis ATH1 genome array, according to the manufacturer’s instruction (Affymetrix).
Scan protocol Arrays were scanned using Agilent GeneArray Scanner.
Description Gene expression data from bzr1-1D;bri1-116 double mutant, repeat 2
Data processing Microarray data were analyzed using Genespring software (version 7, Silicon Genetics). Data that were flagged as absent using mismatch probes were removed from the analysis. GC-RMA signal intensities were generated. However, note that MAS5.0 signal intensities are presented in the table below.
 
Submission date Nov 04, 2010
Last update date Nov 09, 2011
Contact name Yu Sun
E-mail(s) yusun05@gmail.com
Organization name Carnegie Institution of Washington
Department plant biology
Lab Zhiyong wang
Street address 260 panama street
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL198
Series (2)
GSE25134 Expression data from dark-grown BR double mutant bzr1-1D;bri1-116, single mutant bri1-116, and wildtype
GSE25135 Brassinosteroid (BR) plant hormone signaling

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity

Data table
ID_REF VALUE
AFFX-BioB-5_at 293.9
AFFX-BioB-M_at 308.1
AFFX-BioB-3_at 199.1
AFFX-BioC-5_at 781.9
AFFX-BioC-3_at 729.0
AFFX-BioDn-5_at 1674.0
AFFX-BioDn-3_at 2477.6
AFFX-CreX-5_at 10412.8
AFFX-CreX-3_at 13068.8
AFFX-DapX-5_at 6.3
AFFX-DapX-M_at 5.6
AFFX-DapX-3_at 9.7
AFFX-LysX-5_at 17.7
AFFX-LysX-M_at 26.0
AFFX-LysX-3_at 34.6
AFFX-PheX-5_at 3.8
AFFX-PheX-M_at 6.4
AFFX-PheX-3_at 8.8
AFFX-ThrX-5_at 8.2
AFFX-ThrX-M_at 18.6

Total number of rows: 22810

Table truncated, full table size 349 Kbytes.




Supplementary file Size Download File type/resource
GSM617573.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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