|
| Status |
Public on Jun 30, 2016 |
| Title |
12hGX_500pM_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Gene expression after 12 h in 500 pM emamectin benzoate exposed Daphnia magna replicate 3
|
| Organism |
Daphnia magna |
| Characteristics |
tissue: Whole organism
developmental stage: <24h juvenile
|
| Treatment protocol |
Daphnia magna were exposed 5 concentrations of emamectin benzoate for 12h. After exposure, the organisms were pooled and sampled in RNALater (Qiagen, Hilden, Germany) and stored in -80°C until further use.
|
| Growth protocol |
OECD Test Guideline 202
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from pooled Daphnia using Zymo Tissue&Insect RNA kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s instructions.The RNA quality (purity and yield) was controlled by photometric analyses (260/280>1.8, yield >50 ng/μL) using Nanodrop® spectrophotometer (ND-1000, Nanodrop Technologies, Wilminton, Delaware, USA) and RNA integrity 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 50 ng total RNA using Agilent Low Input Quick Amp Labeling Kit (Agilent technologies, Santa Clara, California, USA). The cRNA dye incorporation and yiled 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 |
Gene expression after 12 h in 500 pM emamectin benzoate exposed Daphnia magna
|
| Data processing |
The microarray scan images (raw signal intensity) were extracted using Agilent Feature Extraction software v10.7. Raw data were normalization (quantile) and statistical analyses were performed using GeneSpring GX v11.0 (Agilent Technologies). Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Jun 29, 2016 |
| Last update date |
Jun 30, 2016 |
| Contact name |
Knut Erik Tollefsen |
| E-mail(s) |
ket@niva.no
|
| Organization name |
Norwegian Institute for Water Research (NIVA)
|
| Street address |
Gaustadallèen 21
|
| City |
Oslo |
| ZIP/Postal code |
N-0349 |
| Country |
Norway |
| |
|
| Platform ID |
GPL22095 |
| Series (1) |
| GSE83859 |
Whole organism transcriptomic analysis provides mechanistic insight into the acute toxicity of emamectin benzoate in Daphnia magna |
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