|
| Status |
Public on Jan 06, 2016 |
| Title |
liver-low density-replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
liver-low density-replicate1
|
| Organism |
Coregonus maraena |
| Characteristics |
tissue: liver
gender: mixed
age: 205 days post hatch
|
| Treatment protocol |
Fish (21.6 ± 1.4 cm in length, and 92.0 ± 24.7 g in weight ) were randomly allocated to identical 300-L glass tanks (0.74 m length × 0.58 m width × 0.72 m height; MD, ED, LD or HD conditions), receiving brackish water from the Darss-Zingst Bodden chain (2.5–6 practical salinity units) to the recirculating aquaculture system with an exchange rate of about 0.5 times per hour. Fish were randomly sampled using hand nets. Anaesthetization of fish with was done using phenoxyethanol prior to tissue sampling.
|
| Growth protocol |
Fish were grown in water recirculation tanks at the Institute for Fisheries in Born, Germany.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver, spleen, kidney were sampled. RNeasy Mini Kit (Qiagen, Hilden, Germany) in complement with the RNase-free DNase Set (Qiagen) allowed us to obtain high-quality RNA suitable for microarray hybridizations and quantitative real-time PCR (qPCR) assays.
|
| Label |
Cy3
|
| Label protocol |
Seven individual RNA samples from the same tissue (liver, spleen, kidney) and treatment (MD, ED, LD, HD) were pooled. 100 ng of each total RNA samples was amplified and labeled with the fluorescent dye cyanine 3 using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies). Yields of cRNA and the dye-incorporation rate were measured.
|
| |
|
| Hybridization protocol |
The hybridization procedure was performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Equal amount of fragmented Cy3-labeled cRNA (0.6 µg) in hybridization buffer was hybridized at 65 °C for 17 h to 8×60 K Whole Salmon Genome Oligo Microarrays (AMADID 049158; Agilent Technologies) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 at 37 °C for 1 min.
|
| Scan protocol |
Fluorescence signals of the hybridized Agilent Microarrays were detected using the Microarray Scanner System G2505C (Agilent Technologies).
|
| Description |
Pool of 7 individual RNAs
|
| Data processing |
The Agilent Feature Extraction Software 10.7.3.1 was used to read out and process the microarray image files using default settings. FES corrected the background based on a two-sided Student t-test.
|
| |
|
| Submission date |
Jan 05, 2016 |
| Last update date |
Mar 30, 2017 |
| Contact name |
Alexander Rebl |
| E-mail(s) |
rebl@fbn-dummerstorf.de
|
| Phone |
+493820868721
|
| Organization name |
Research Institute for Farm Animal Biology
|
| Department |
Institute of Genome Biology
|
| Lab |
Fish Genetics
|
| Street address |
Wilhelm-Stahl-Allee 2
|
| City |
Dummerstorf |
| ZIP/Postal code |
18196 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21057 |
| Series (1) |
| GSE76543 |
Potential biomarker genes for crowding stress in maraena whitefish Coregonus maraena |
|
