|
| Status |
Public on Sep 01, 2013 |
| Title |
HAN-4h-rep4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RNA from 4h DEX treatment
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: HAN overexpression
time: 4h
|
| Growth protocol |
Plants used for microarray experiments were 35S:HAN-GR lines in the Landsberg erecta (Ler) background.Plants were grown on a soil:vermiculite:perlite mixture under continuous illumination with a light intensity range of 80 to 100 µmol•m–2•s–1 at 20°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using Qiagen RNeasy according to the manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
RNA was dye-labeled as previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). In brief, first and second strand cDNA was synthesized using a poly(A)-primer with a T7 promoter sequence. Then, in vitro transcription was performed using the Megascript T7 kit (Ambion, Austin, TX). For the oligonucleotide array, dye molecules were coupled to the amplified RNA, and the dye-labeled RNA was fragmented before hybridization.
|
| |
|
| Channel 2 |
| Source name |
RNA from 4h mock
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: control
time: 4h
|
| Growth protocol |
Plants used for microarray experiments were 35S:HAN-GR lines in the Landsberg erecta (Ler) background.Plants were grown on a soil:vermiculite:perlite mixture under continuous illumination with a light intensity range of 80 to 100 µmol•m–2•s–1 at 20°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using Qiagen RNeasy according to the manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
RNA was dye-labeled as previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). In brief, first and second strand cDNA was synthesized using a poly(A)-primer with a T7 promoter sequence. Then, in vitro transcription was performed using the Megascript T7 kit (Ambion, Austin, TX). For the oligonucleotide array, dye molecules were coupled to the amplified RNA, and the dye-labeled RNA was fragmented before hybridization.
|
| |
|
| |
| Hybridization protocol |
Dye-labeled antisense RNA was hybridized to microarrays using a MAUI hybridization system (BioMicro Systems, Salt Lake City, UT, USA) as previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). Specifically, hybridizations were done as follows: dye-labeled antisense RNA preparations were dried down and the resulting pellets were re-suspended in 5 ul 10 mM EDTA and 45 ul SlideHyb Buffer #1 (Ambion, Austin, Texas, United States) and hybridized for 14 h to microarrays at 48C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah, United States) according to the manufacturer's instructions.
|
| Scan protocol |
Microarrays were scanned and the data acquired with an Axon GenePix 4200A scanner using GenePix v5.0 analysis software.
|
| Description |
Biological replicate 4 of 4.
|
| Data processing |
Data were processed using lowess normalization with the Resolver data analysis system (Rosetta Biosoftware, Seattle, WA).
|
| |
|
| Submission date |
Jun 12, 2012 |
| Last update date |
Sep 01, 2013 |
| Contact name |
Xiaolan Zhang |
| E-mail(s) |
zhxiaolan@cau.edu.cn
|
| Organization name |
China Agricultural University
|
| Department |
Vegetable Science
|
| Street address |
No.2 Yuanmingyuan Xi Lu Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL5762 |
| Series (1) |
| GSE38658 |
Transcription repressor HANABA TARANU (HAN) controls flower development via integrating multiple hormone actions, floral organ specification and GATA3 family auto-regulation |
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