|
| Status |
Public on Nov 15, 2023 |
| Title |
WholeRoot_625µMP_0d_rep2 [sP0d.2] |
| Sample type |
RNA |
| |
|
| Source name |
Whole root, 625 µM P, 0 days, replicate 2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole root
treatment: 625 µM P
time after treatment: 0 days
|
| Treatment protocol |
Seven-day-old seedlings precultured on sufficient phosphorus were transferred to fresh solid half-strength Murashige and Skoog medium containing 625 µM KH2PO4 (sufficient P) or 100 µM KH2PO4 (deficient P). The missing potassium in the P-deficient medium was supplied as KCl.
|
| Growth protocol |
Seeds of Arabidopsis thaliana (Columbia-0, CS60000) were surface sterilized in 70% (v/v) ethanol and 0.05% (v/v) Triton X-100. Seedlings were first germinated for seven days on agar plates containing 0.5% (w/v) sucrose and 1% (w/v) agar before seedlings of similar sizes were transferred to treatments containing identical sucrose and agar concentrations. The nutrient composition was half-strenght Murashige and Skoog and Difco agar (Becton Dickinson; cat. number 214541;) was used as gelling agent. In the preculture, 625 µM P was supplied as KH2PO4. In treatment plates, the solid half-strength MS medium contained 625 µM P (sufficient P) or 100 µM P (deficient P), with 525 µM K being supplied as KCl. Each treatment plate contained 10 seven-day-old seedling. Each replicate was composed of 5 plates containing 10 seven-day-old seedling each (i.e., 50 plants pooled as one replicate). Agar plates were sealed with Leukopor tape (Smith & Nephew) and placed vertically in a randomized block design within a growth cabinet (Percival Scientific) with 22°C day and 19°C night temperatures and a 10-h light period with a light intensity of 120 µmol photons m-2 s-1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from whole roots (roots of 50 plants pooled togeher to form one replicate) using an RNeasy plant mini kit (Qiagen) with on-column DNase treatment according to the manufacturer’s instructions. cDNA was prepared using random hexamer primers and SuperScript II reverse transcriptase (Life Technologies) according to the manufacturer’s protocol.
|
| Label |
Cy3
|
| Label protocol |
RNA amplification, labeling and hybridization to Agilent microarrays (Arabidopsis (V4, 021169) Gene Expression Microarray) were conducted following the manufacturer’s protocol (Agilent Technologies).
|
| |
|
| Hybridization protocol |
RNA amplification, labeling and hybridization to Agilent microarrays (Arabidopsis (V4, 021169) Gene Expression Microarray) were conducted following the manufacturer’s protocol (Agilent Technologies).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides.
|
| Description |
Gene expression after 0 days of 625 µM posphate treatment
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 021169_D_F_20140929) to obtain background subtracted and spatially detrended Processed Signal intensities. Analysis of microarray data was performed with the R package limma. Raw feature intensities were background corrected using “normexp”, and “quantile” normalization method was used to normalize between arrays.
|
| |
|
| Submission date |
Nov 11, 2022 |
| Last update date |
Nov 15, 2023 |
| Contact name |
Anja Hartmann |
| E-mail(s) |
hartmann@ipk-gatersleben.de
|
| Phone |
+49 39482 5-578
|
| Organization name |
IPK Gatersleben
|
| Department |
PZB
|
| Lab |
MPE
|
| Street address |
Corrensstraße 3
|
| City |
Seeland |
| State/province |
Saxony-Anhalt |
| ZIP/Postal code |
06466 |
| Country |
Germany |
| |
|
| Platform ID |
GPL12621 |
| Series (1) |
| GSE217790 |
Expression signatures of Arabidopsis thaliana roots under low or high phosphate conditions. |
|
