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Status |
Public on Nov 15, 2023 |
Title |
WholeRoot_625µMP_1d_rep2 [sP1d.2] |
Sample type |
RNA |
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Source name |
Whole root, 625 µM P, 1 days, replicate 2
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Organism |
Arabidopsis thaliana |
Characteristics |
tissue: whole root treatment: 625 µM P time after treatment: 1 day
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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.
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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.
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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.
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Label |
Cy3
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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).
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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).
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Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides.
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Description |
Gene expression after 1 day of 625 µM posphate treatment
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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.
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Submission date |
Nov 11, 2022 |
Last update date |
Nov 15, 2023 |
Contact name |
Anja Hartmann |
E-mail(s) |
hartmann@ipk-gatersleben.de
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Phone |
+49 39482 5-578
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Organization name |
IPK Gatersleben
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Department |
PZB
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Lab |
MPE
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Street address |
Corrensstraße 3
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City |
Seeland |
State/province |
Saxony-Anhalt |
ZIP/Postal code |
06466 |
Country |
Germany |
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Platform ID |
GPL12621 |
Series (1) |
GSE217790 |
Expression signatures of Arabidopsis thaliana roots under low or high phosphate conditions. |
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