|
| Status |
Public on Feb 09, 2017 |
| Title |
Zebrafish_96h_ZnSO4-LC25_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Zebrafish, 96h, ZnSO4-LC25, replicate 2
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Whole body
age: 96hr
|
| Growth protocol |
The zebrafish embryo (96h) was exposed to LC25 concentration of ZnO NPs and ZnSO4 (2.64 and 7.75 mg/L, respectively)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA (specific activity >10 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Zebrafish Gene Expression Microarrays (G2519F) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then air-dried by slowly removing the slide rack minimizing droplets on the slides.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression after 96hr in ZnSO4-LC25-treated zebrafish
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026437_D_F20130127) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Jan 22, 2016 |
| Last update date |
Feb 09, 2017 |
| Contact name |
June-Woo Park |
| E-mail(s) |
jwpark@kitox.re.kr
|
| Organization name |
Korea Institute of Toxicology
|
| Department |
Environmental Risk Research
|
| Street address |
17, Jegok-gil, Munsan-eup
|
| City |
Jinju |
| ZIP/Postal code |
52834 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21361 |
| Series (1) |
| GSE77148 |
Comparisons of toxicogenomic responses in zebrafish (Danio rerio) exposed to ZnO nanoparticles and ZnSO4: The impact of sublethal concentration (LC25) on global gene expression profiles |
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