GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM617580 Query DataSets for GSM617580
Status Public on Dec 31, 2010
Title Col, rep3
Sample type RNA
Source name Columbia control
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia-0 (Col-0)
genotype/variation: wildtype
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 wildtype control, 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
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
VALUE MAS5.0 signal intensity

Data table
AFFX-BioB-5_at 230.0
AFFX-BioB-M_at 222.4
AFFX-BioB-3_at 152.4
AFFX-BioC-5_at 636.1
AFFX-BioC-3_at 465.6
AFFX-BioDn-5_at 1230.5
AFFX-BioDn-3_at 1973.4
AFFX-CreX-5_at 7268.9
AFFX-CreX-3_at 9286.4
AFFX-DapX-5_at 14.3
AFFX-DapX-M_at 21.5
AFFX-DapX-3_at 5.5
AFFX-LysX-5_at 11.4
AFFX-LysX-M_at 7.3
AFFX-LysX-3_at 28.4
AFFX-PheX-5_at 4.0
AFFX-PheX-M_at 12.1
AFFX-PheX-3_at 10.6
AFFX-ThrX-5_at 4.3
AFFX-ThrX-M_at 8.1

Total number of rows: 22810

Table truncated, full table size 350 Kbytes.

Supplementary file Size Download File type/resource
GSM617580.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap