|
| Status |
Public on Oct 01, 2007 |
| Title |
wild-type at T0, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis wild-type root, no nitrate induction
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Columbia ecotype, root tissue of 10-day-old seedlings
|
| Treatment protocol |
10-day-old plants were shifted to 60 mL of the same 12.5 mM (NH4)2 succinate medium in which the pH had been changed to 5.5 by addition of HCl. After 3 h treatment, the plants were washed twice with 10 mM K2HPO4/KH2PO4, pH 5.5, then 1) collected the root sample (T0), or 2) shifted for 0.5 hour (T0.5) to 60 mL of the same pH 5.5 growth medium, but with the 12.5 mM (NH4)2 succinate replaced by 25 mM KNO3, and the root sample was collected after 30 min induction.
|
| Growth protocol |
Approximately 100 sterilized seeds of Arabidopsis thaliana wild-type and chl1-5 plants (Columbia ecotype) were grown in different areas on the same mesh in a Magenta vessel (Sigma) in 60 mL of NO3--free liquid growth medium (10 mM K2HPO4/KH2PO4 pH 5.5, 2 mM MgSO4, 0.1 mM FeSO4-EDTA, 1 mM CaCl2, 50 μM H3BO3, 12 μM MnSO4•H2O, 1 μM ZnCl2, 1 μM CuSO4•5H2O, 0.2 μM Na2MoO4•2H2O, 1 g/L MES, 0.5% sucrose) containing 12.5 mM (NH4)2 succinate as the sole nitrogen source, pH 6.5. For each biological replicate, 9 vessels ( ~ 900 seedlings / each replicate) of samples were pooled to use in a single independent experiment. Plants were grown under continuous illumination at 24-26°C and rotated at 100 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol Reagent (Invitrogen Life Technology, Grand Island, NY, U.S.A.) according to the manufacturer’s instructions, followed by chloroform extraction and isopropanol / EtOH precipitation. The total RNA was further purified using an RNeasy Plant Mini Kit (Qiagen, Chatsworth, CA)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix ATH1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip scanner 3000.
|
| Description |
Gene expression data from wild-type plant before 25 mM nitrate induction, biological replicate 1.
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
|
| |
|
| Submission date |
Sep 24, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Yi-Fang Tsay |
| E-mail(s) |
yftsay@gate.sinica.edu.tw
|
| Phone |
+886-2-27899198
|
| Organization name |
Academia Sinica
|
| Department |
Institute of Molecular Biology
|
| Lab |
N317
|
| Street address |
128 Sec. 2, Academia Rd, Nankang
|
| City |
Taipei |
| ZIP/Postal code |
11529 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE9148 |
Expression data of 10-day-old wild-type and chl1-5 plants exposed to 25 mM nitrate for 0h or 0.5h |
|
| Relations |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
