|
| Status |
Public on Mar 31, 2021 |
| Title |
Arabidopsis_ab_low_150min_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Rosette leaves of Arabidopsis thariana AB plant which exposed to 1-2 ppm of formaldehyde for 150 minutes.
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
genotype: AB
age: 7-week old
tissue: Rosette leaf
|
| Treatment protocol |
After the acclimation of plants, formaldehyde exposure experiments were started at 0:30 p.m. and finished at 3:00 p.m. For the exposure, 3 plants were placed into the chamber (volume: 10 L) each exposure condition and these plants were treated as replications. During exposure, the chamber was ventilated by gas that was adjusted to each exposure concentration at flow rate of 200 ml/min, and kept humidity of 50-60% at 24oC under the light (approx. 70 µmol/m2/sec.). The exposure condition was non-treatment (acclimation condition, outside of the exposure chamber, less than 0.08 ppm), air-control (less than 0.04 ppm), low-concentration (1-2 ppm) and high-concentration (14-16 ppm). The rosette leaves of the exposed plants (approx. 100 mg/each sample) were placed into vials and were frozen by liquid nitrogen immediately.
|
| Growth protocol |
Seeds of Arabidopsis thariana AB plants were sown on modified MS-agar medium (half strength inorganic compounds for MS medium, 1.5 mg/L thiamine-HCl, 2.5 mg/L pyridoxine-HCl, 0.25 mg/L nicotinic acid, 15 g/L sucrose, 8 g/L agar and adjusted to pH 5.8 with KOH) containing 30 mg/L kanamycin and 40 mg/L gentamicin. After 1 week, the selected seedlings were transferred to the modified MS-agar medium without antibiotics, and were grown for 2 weeks. The 3-week old plants were transferred and grown in inorganic soil (ratio of vermiculite to perlite was 2 to 1) that absorbed 1 ml/L HYPONeX (HYPONeX Japan, Osaka, Japan) for 4 weeks at 22oC under 10 hours light (70-100 µmol/m2/sec.) in an incubator. For the acclimation before exposure, the 7-week old plants were kept under constant light (approx. 70 µmol/m2/sec.) at 24oC for 72 hours from 0:30 p.m. The plants were exposed to formaldehyde after 72 hours of acclimation. The environmental formaldehyde concentration was kept at less than 0.08 ppm until plants’ growth and experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 100 mg of rosette leaves was applied to total RNA extraction using Plant RNA isolation mini kit (Agilent) under its protocol.
|
| Label |
Biotin
|
| Label protocol |
Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.
|
| |
|
| Hybridization protocol |
Standard Affymetrix procedures.
|
| Scan protocol |
Standard Affymetrix procedures.
|
| Description |
Gene expression data from rosette leaves of Arabidopsis thaliana AB plant 7-week old that exposed to 1-2 ppm of formaldehyde for 150 minutes.
|
| Data processing |
The data were analyzed with R/Bioconductor using GC-RMA by gcrma package as normalization method.
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| |
|
| Submission date |
Mar 12, 2010 |
| Last update date |
Mar 31, 2021 |
| Contact name |
Katsura Izui |
| E-mail(s) |
izui@waka.kindai.ac.jp
|
| Phone |
+81-75-491-3960
|
| Organization name |
Kinki University
|
| Department |
School of Biology-oriented Science and Technology
|
| Street address |
930 Nishimitani
|
| City |
Kinokawa |
| State/province |
Wakayama |
| ZIP/Postal code |
649-6493 |
| Country |
Japan |
| |
|
| Platform ID |
GPL198 |
| Series (2) |
| GSE20865 |
Expression data from rosette leaves of Arabidopsis thaliana which has formaldehyde tolerance (rmpA/rmpB double transgenic) upon formaldehyde exposure |
| GSE20866 |
Expression data from rosette leaves of Arabidopsis thaliana wild type and rmpA/rmpB double transgenic exposed to formaldehyde |
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