|
| Status |
Public on Oct 14, 2015 |
| Title |
DU_replicate4 |
| Sample type |
RNA |
| |
|
| Source name |
0.25 mg/L depleted uranium (DU) exposed
|
| Organism |
Salmo salar |
| Characteristics |
stress: 0.25 mg/L depleted uranium (DU)
tissue: Liver
|
| Treatment protocol |
Atlantic salmon parr were transferred to lake water (Maridalsvannet, Norway) for 72 h acclimation prior to being exposed to control, 70 mGy external gamma radiation emitted from a cobalt-60 source, and 0.25 mg/L depleted uranium in the dark for 48 h. Fish were exposed in a flow-through system supplied with air pumps. No feeding was performed during the acclimation and exposure period.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 20-30 mg snap-frozen liver tissue using RNeasy Plus Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.The RNA quality (purity and yield) was controlled by photometric analyses (260/230 > 2.0, 260/280>1.8, yield >200 ng/μL) using Nanodrop® spectrophotometer (ND-1000, Nanodrop Technologies, Wilminton, Delaware, USA) and RNA integrity (RIN>8.0) inspected by Bioanalyzer gelelectrophoresis with RNA 6000 Nano chips (Agilent technologies, Santa Clara, California, USA) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Cyanine 3-CTP (Cy3) labeled cRNA was made from 200 ng total RNA using Agilent Low Input Quick Amp Labeling Kit (Agilent technologies, Santa Clara, California, USA). The cRNA dye incorporation and yield were checked using Agilent Bioanalyzer (Agilent Technologies).
|
| |
|
| Hybridization protocol |
Totally 600 ng of Cy3-labeled, linearly amplified cRNA was fragmented and hybridized to 8x60k microarrays and rotationally (10 rpm) incubated at 65 ºC for 17 h.
|
| Scan protocol |
Microarray slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (Dye channel: G (green), scan region: Agilent HD (61 × 21.6 mm), Scan resolution: 3 µm, Tiff file dynamic range: 20 bit, Green PMI gain: 100%).
|
| Description |
U4
Gene expression after 48 h in 0.25 mg/L depleted uranium exposed fish liver
|
| Data processing |
The microarray scan images (raw signal intensity) were extracted using Agilent Feature Extraction software v10.7. Raw data were normalized (quantile) and statistical analyses were performed using GeneSpring GX v11.0 (Agilent Technologies). Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Oct 14, 2015 |
| Last update date |
Oct 14, 2015 |
| Contact name |
You Song |
| E-mail(s) |
[email protected]
|
| Organization name |
Norwegian Institute for Water Research (NIVA)
|
| Department |
Ecotoxicology and Risk Assessment
|
| Street address |
Økernveien 94
|
| City |
Oslo |
| ZIP/Postal code |
0579 |
| Country |
Norway |
| |
|
| Platform ID |
GPL18864 |
| Series (1) |
| GSE74012 |
Combined hepatic transcriptional effects of gamma radiation and depleted uranium on Atlantic salmon (Salmo salar) |
|
