|
| Status |
Public on Dec 31, 2020 |
| Title |
Rat liver, Control_rep6 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: liver
treatment: Control
dose: 0
dose unit: mg/kg bw/day
way of administration: oral gavage
days of administration: 28
strain: Wistar (Crl:WI)
Sex: F
|
| Treatment protocol |
The chosen doses of the test compounds (imazalil, thiacloprid and clothianidin) were daily administered to the rats by oral gavage through 28-day treatment. Test compounds were suspended in 0.5% aqueous carboxymethyl-cellulose, whereby the specified dosing volume was 7.5 ml/kg bw. Rats of the control group were treated with the vehicle only (0.5% aqueous carboxymethyl-cellulose in deionized water). Dose selection was based on studies from draft assessment report (DAR). Equipotent mixtures were established following the relative potency factors (RPF) approach.
|
| Growth protocol |
Young adult female Wistar rats (Crl:WI) were acclimatized to the laboratory conditions for at least 1 week and were weighed and monitored for their health status. Rats were allocated in a randomized manner to the different treatment groups and were maintained under conventional laboratory conditions: constant 12/12-hour light/dark cycle with controlled temperature at 22°C ± 2°C and humidity at 55% ± 15%.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from approximately 20-40 mg frozen rat tissue sample using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA Sample Preparation-Kit from Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
S825Nr6
|
| Data processing |
Adapters were trimmed by Skewer version 0.2.2.
Data quality was assessed by FastQC version 0.11.5.
Reads were mapped to the rat reference genome Rnor_5.0 and counted per gene ID using STAR version 2.5.2b.
After removing genes with low expression (sum of reads across all samples below two), 19904 genes were retained and analyzed by the R-package DESeq2 version 1.15.1 using default settings estimation of size factors and dispersion.
Negative Binomial GLM fitting and Wald statistics were applied to test for differential gene expression between each treatment and control conditions, respectively. False discovery rate (FDR) was used to control for multiple testing. Only genes with a q-value ≤ 0.05 were included in the further analyses.
Genome_build: Rnor_5.0
|
| |
|
| Submission date |
Jul 07, 2020 |
| Last update date |
Dec 31, 2020 |
| Contact name |
Heike Sprenger |
| E-mail(s) |
Heike.Sprenger@bfr.bund.de
|
| Organization name |
German Federal Institute for Risk Assessment
|
| Department |
Food Safety
|
| Street address |
Max-Dohrn-Strasse 8-10
|
| City |
Berlin |
| ZIP/Postal code |
10589 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE153986 |
Transcriptomic analysis of hepatotoxicity induced by pesticides imazalil, thiacloprid and clothianidin alone or in binary mixtures in a 28-day study in female Wistar rats |
|
| Relations |
| BioSample |
SAMN15469686 |
| SRA |
SRX8684117 |
