|
| Status |
Public on May 15, 2012 |
| Title |
control vs MeHg exposure rep 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
whole organism
|
| Organism |
Danio rerio |
| Characteristics |
strain: wild type AB, Tübingen
tissue: whole embryos
developmental stage: 4 dpf
treatment: fish medium (control)
|
| Treatment protocol |
24 hpf embryos were exposed for 24 hours with 60µg/l MeHg and embryos were maintained in fish medium at 28.5 °C as control
|
| Growth protocol |
adult fish were maintained in fish water at 28.5 °C, subjected to a photoperiod of 10 hours light and 14 hours dark, and fed with dry flake food and brine shrimp. Embryos were kept in embryo medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction following Rneasy Mini Kit (Qiagen)
|
| Label |
Cy3, Cy5
|
| Label protocol |
2 µg of total RNA from each sample (exposure and control embryos) was labelled with Cyanine3 and Cyanine 5-CTP according to Agilent Low RNA Input Linear Amplification Kit.
|
| |
|
| Channel 2 |
| Source name |
whole organism
|
| Organism |
Danio rerio |
| Characteristics |
strain: wild type AB, Tübingen
tissue: whole embryos
developmental stage: 4 dpf
treatment: exposed to 3-4 dpf to 60µg/l MeHg
|
| Treatment protocol |
24 hpf embryos were exposed for 24 hours with 60µg/l MeHg and embryos were maintained in fish medium at 28.5 °C as control
|
| Growth protocol |
adult fish were maintained in fish water at 28.5 °C, subjected to a photoperiod of 10 hours light and 14 hours dark, and fed with dry flake food and brine shrimp. Embryos were kept in embryo medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction following Rneasy Mini Kit (Qiagen)
|
| Label |
Cy5, Cy3
|
| Label protocol |
2 µg of total RNA from each sample (exposure and control embryos) was labelled with Cyanine3 and Cyanine 5-CTP according to Agilent Low RNA Input Linear Amplification Kit.
|
| |
|
| |
| Hybridization protocol |
The hybridistaion of labelled probes was performed following Agilent Microarray hyridisation Kit.
|
| Scan protocol |
Samples were scanned on Axon 4000B scanner and the images analysed used GenePix Pro 61
|
| Description |
biological repeat
|
| Data processing |
The data was analysed using Matlab R2009b, data is background substracted, log2-values calculated and LOWESS- and centering normalized was perfomed. Dye-swaps were combined. Samples were labeled with Cy5 exposed, Cy3 control. Reverse is true for _swap.gpr raw data files.
|
| |
|
| Submission date |
May 14, 2012 |
| Last update date |
May 17, 2012 |
| Contact name |
Jessica Legradi |
| Organization name |
Karlsruhe Institute of Technology
|
| Department |
Institute of Toxicology and Genomics ITG
|
| Lab |
Straehle
|
| Street address |
Hermann-von-Helmholtz-Platz 1
|
| City |
Eggenstein-Leopoldshafen |
| State/province |
Baden-Wuerttemberg |
| ZIP/Postal code |
76344 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6563 |
| Series (1) |
| GSE37970 |
MeHg exposure zebrafish embryos vs control |
|
