|
| Status |
Public on Nov 05, 2019 |
| Title |
C1_F2 (IM study) |
| Sample type |
RNA |
| |
|
| Source name |
4 months old zebrafish liver
|
| Organism |
Danio rerio |
| Characteristics |
tissue: liver
age: 4 months old
gender: female
treatment: IM, 0.01 µg/L
|
| Treatment protocol |
Imatinib mesylate (sc-202180A, Santa Cruz Biotechnology) was diluted in the clean recirculation system water to final concentrations of the exposure of 0.01 µg/L (C1) and 1.0 µg/L (C2). The control group was grown in the recirculation system water alone. All of the treatments, including the controls, were carried out in duplicate. The experiment was performed under the semistatic conditions with a complete renewal of exposure medium every three days. At the age of 4 months, part of F1 fish was sampled for gene expression analyses.
|
| Growth protocol |
The wild time (AB line) of zebrafish (Danio rerio) originated and was cultured at the Department of Aquaculture of Szent István University (Hungary). Prior to the study, the parent generation was maintained in a recirculation system that allowed continuous flow of water (ZebTec; Tecniplast Inc.) under a light regime of 14 h light/ 10 h dark. The parameters of the recirculation system water were as follows: temperature, 25 ±0.5 °C; pH, 7.4 ±0.2; and conductivity, 525 ±50 µS. During the study period, the zebrafish were maintained at 24 °C to 26 °C under a light regime of 14 h light/ 10 h dark. Fish were fed twice a day with SDS Small Gran granulated feed and twice a week, with Artemia. The animal protocol was approved by the Hungarian Animal Welfare Law .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was isolated by Direct-zol RNA Miniprep (ZymoResearch) from liver of 6 individuals liver per exposure point from each of the two replicates. After RNA quality and quantity evaluation (Agilent Bioanalyzer, RNA 6000 Nano Kit, Eukaryote Assay), RNA from 1-3 individuals from same treatment, replicate and gender was pooled, DNase treated (Invitrogen DNaseI; 0.2 U/µg RNA) in 45 μl reactions and subsequently purified using RNeasy Mini Elute kit (Qiagen). Purified RNA was checked for integrity and quantity by Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
Labelling, hybridization and scanning were performed by the IMGM (Germany). The total RNA was labelled with Cy-3 using Low Input Quick-Amp Labeling Kit One-Color (Agilent technologies) following manufacturers protocol
|
| |
|
| Hybridization protocol |
Hybridizations and washes were performed using Gene Expression Hybridization Kit (Agilent Technologies) following manufactures protocol
|
| Scan protocol |
Hybridized slides were scanned on Agilent DNA Microarray Scanner and signals were extracted and quality control was performed using Feature Extraction 10.7.3.1 Software (Agilent Technologies).
|
| Description |
pool of 2 individuals
|
| Data processing |
Microarray data analysis was performed in R environment (version 2.15.1) using Bioconductor’s libraries limma and vsn.
|
| |
|
| Submission date |
Jul 14, 2016 |
| Last update date |
Nov 05, 2019 |
| Contact name |
Spela Baebler |
| E-mail(s) |
spela.baebler@nib.si
|
| Organization name |
National Institute of Biology
|
| Department |
Department of Biotechnology and Systems Biology
|
| Street address |
Vecna pot 111
|
| City |
Ljubljana |
| ZIP/Postal code |
1000 |
| Country |
Slovenia |
| |
|
| Platform ID |
GPL14664 |
| Series (1) |
| GSE84394 |
Zebrafish liver transcriptome in response to chronic treatment with environmentally relevant concentrations of imatinib mesylate |
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