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Sample GSM617577 Query DataSets for GSM617577
Status Public on Dec 31, 2010
Title bri1-116, rep3
Sample type RNA
 
Source name Homozygote bri1-116
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia-0 (Col-0)
genotype/variation: bri1-116 null 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 Seedlings 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 the Plant RNA Purification Reagent (Invitrogen), treated with RNase-free DNase I (Qiagen), and cleaned up using the 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 the Arabidopsis ATH1 genome array according to the manufacturer’s instructions (Affymetrix).
Scan protocol Arrays were scanned using the Agilent GeneArray Scanner.
Description Gene expression data from bri1-116 null mutant, repeat 3.
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 (3)
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
GSE25396 Expression data from dark-grown AtGATA2 (At2g45050) overexpression transgenic line, homozygous bri1-116 and Col-0 wild type

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity

Data table
ID_REF VALUE
AFFX-BioB-5_at 302.8
AFFX-BioB-M_at 314.7
AFFX-BioB-3_at 206.5
AFFX-BioC-5_at 974.9
AFFX-BioC-3_at 759.4
AFFX-BioDn-5_at 1561.4
AFFX-BioDn-3_at 3001.4
AFFX-CreX-5_at 9597.6
AFFX-CreX-3_at 14834.3
AFFX-DapX-5_at 2.2
AFFX-DapX-M_at 5.6
AFFX-DapX-3_at 6.0
AFFX-LysX-5_at 2.3
AFFX-LysX-M_at 26.2
AFFX-LysX-3_at 33.7
AFFX-PheX-5_at 3.4
AFFX-PheX-M_at 6.4
AFFX-PheX-3_at 31.1
AFFX-ThrX-5_at 32.3
AFFX-ThrX-M_at 3.5

Total number of rows: 22810

Table truncated, full table size 349 Kbytes.




Supplementary file Size Download File type/resource
GSM617577.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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