|
| Status |
Public on Mar 23, 2015 |
| Title |
LPS_Stimulated_Overfed_Zebrafish_Liver_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Liver Diet Induced Obesity LPS Stimulated Adult Zebrafish 3hpi
|
| Organism |
Danio rerio |
| Characteristics |
diet: Overfed
stimulated with: 10 μg of pure LPS
time point: 3 hours post injection (hpi)
tissue: liver
|
| Treatment protocol |
Control fish were fed two times a day, one with Artemia and the other with standard fish chow while obese fish were fed fish chow two more times a day. After 8 months of differential diet, PBS or 10 μg of pure LPS (Sigma) was intraperitoneally injected in both control and obese fish. For every treatment, 4 biological replicates of livers from 3 fish were pooled 3 hours post injection and conserved at -80ºC until use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with TRIzol reagent (Life Technologies, Madrid, Spain) following the TRIzol manufacturer’s specifications in combination with the RNeasy Mini Kit (Qiagen, Madrid), and preserved at -80 ºC until use. After DNase I treatment, RNA quality was assessed with the Agilent 2100 Bioanalyzer and kept frozen at -80 °C until all of the experiments could be hybridized and processed simultaneously.
|
| Label |
Cy3
|
| Label protocol |
Total RNA (500 ng) was amplified and Cy3-labeled with Agilent’s One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit according to manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Each amplified and labelled sample was briefly hybridized at 65 °C for 17 hours following manufacturer instructions.
|
| Scan protocol |
Microarray slides were scanned with Agilent Technologies Scanner model G2505B.
|
| Description |
LPS_Overfed_Zebrafish_1
|
| Data processing |
Spot intensities and other quality control features were extracted with the Feature Extraction software version 10.4.0.0 (Agilent). The results for the fluorescence intensity data and quality annotations were imported into GeneSpring GX version 12.6 (Agilent Technologies). All of the control features (including the positive and negative controls and the landing lights) were excluded from subsequent analyses. Normalization was then carried out by a percentile shift at the 75th percentile. Entities with an expression between the 20 and 95th percentile in the raw data were retained and further analyzed at gene level (i.e. merging the signal values of the different probes for the same gene). The gene-level analysis results are provided in the 'gene_level_analysis.txt' along with the data processing details in the 'readme.txt'.
|
| |
|
| Submission date |
Apr 02, 2014 |
| Last update date |
Mar 24, 2015 |
| Contact name |
Gabriel Forn-Cuní |
| Organization name |
Universiteit Leiden
|
| Department |
IBL-ASH-CO
|
| Street address |
Einsteinweg 55
|
| City |
Leiden |
| State/province |
Zuid-Holland |
| ZIP/Postal code |
2313JA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL14664 |
| Series (1) |
| GSE56478 |
Effect of obesity on liver immune response to inflammatory stimuli in a diet-obesity model of zebrafish (Danio rerio) |
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