|
| Status |
Public on Sep 10, 2019 |
| Title |
hda19 non-stress rep. 1 |
| Sample type |
RNA |
| |
|
| Source name |
hda19 non-stress
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
gentoype/variation: hda19 mutant
ecotype: Col-0
condition: non-stress
|
| Treatment protocol |
The salt treatment was performed at 5 day after germination in 125 mM NaCl condition. Samples were collected at 2 h after the NaCl treatment.
|
| Growth protocol |
Seeds of Arabidopsis thaliana (hda19, quad, quint, Col-0 ecotype) were grown on liguid MS medium containing 0.1% pure Agar at 22°C under 16-h-light/8-h-dark for 5 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from at least three biological replicates with the RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer’s instructions
|
| Label |
Cy3
|
| Label protocol |
Fluorescent-labeled (Cy3) cRNAs were prepared from 400 ng total RNA from each sample using a Quick Amp labeling kit (Agilent Technologies)
|
| |
|
| Hybridization protocol |
600 ng of cRNAs were hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer (Agilent), and then dried immediately by brief centrifugation.
|
| Scan protocol |
The microarray was scanned by Agilent DNA Microarray Scanner G2505B and raw data was extracted using Feature Extraction program ver 9.1.
|
| Description |
Col-0
|
| Data processing |
RMA normalization was performed for signals of microarray probes using limma package (Ritchie et al., 2015) on R 2.12.1 program.
|
| |
|
| Submission date |
Oct 15, 2018 |
| Last update date |
Sep 12, 2019 |
| Contact name |
Minoru Ueda |
| E-mail(s) |
[email protected]
|
| Organization name |
RIKEN
|
| Department |
CSRS
|
| Lab |
Plant Genomic Network Research Team
|
| Street address |
1-7-22 Suehiro-cho, Tsurumi-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL22706 |
| Series (1) |
| GSE121225 |
Transcriptome analysis of the hierarchical response of HDAC proteins that respond in an antagonistic manner to salinity stress |
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