|
| 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 |
| 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 |
|
