XomeTox - Multi-omics data sets
Workpackage 1 focuses on the collection of multi-omics data sets and their subsequent evaluation by means of multi-omics data integration methods.
What follows is a summary of multi-omics data sets in a toxicological setting that are used in WP1:
1. murine hepatocytes
- compound: benzo[a]pyrene
- concentration: 50nM, 5000nM
- timepoints: 2h, 4h, 8h, 12h, 24h
- transcriptome:
- proteome:
- Kalkhof et al. (2015)
- pubmed ID: 25362887
- in-house data
- metabolome:
- Kalkhof et al. (2015)
- pubmed ID: 25362887
- in-house data
2. human HepG2 cell line
- compound: ketoconazole
- transcriptome:
- Open TG-Gates data set (ref)
- concentration: 600nM, 3000nM, 15000nM
- timepoints: 2h, 8h, 24h
- proteome:
- Wewering et al. (2017)
- pubmed ID: 26965496
- concentration: 1000nM, 10000nM
- timepoints: 24h
- in-house data
- metabolome:
- Wewering et al. (2017)
- pubmed ID: 26965496
- concentration: 1000nM, 10000nM
- timepoints: 24h
- in-house data
3. NanoParticle
- compound: titanium dioxide (TiO2)
- transcriptome:
- proteome:
- data from UFZ project NanoToxClass
- not published, in-house data
- tissue: human alveolar epithelial cells RLE-6TN
- concentration: 10000ng/cm3
- timepoints: 24h after exposure
- metabolome
- data from UFZ project NanoToxClass
- not published, in-house
- tissue: human alveolar epithelial cells RLE-6TN
- concentration: 10000ng/cm3
- timepoints: 24h after exposure
4. NanoParticle
- compound: silicone dioxide (SiO2)
- transcriptome:
- proteome:
- data from UFZ project NanoTox Class
- not published, in-house
- tissue: human alveolar epithelial cells RLE-6TN
- concentration: 10000ng/cm3
- timepoints: 24h after exposure
- metabolome:
- data from UFZ project NanoTox Class
- not published, in-house
- tissue: human alveolar epithelial cells RLE-6TN
- concentration: 10000ng/cm3
- timepoints: 24h after exposure
5. Pregninolone carbonitrile
- Nagahori et al. (2017)
- pubmed ID: 28825834
- organism: Rattus norvegicus
- compound: pregninolone carbonitrile
- tissue: liver homogenate
- transcriptome:
- NCBI GEO: GSE95475
- concentration: 100 mg/kg/day
- exposure: 7 days
- timepoints: after 7 days
- proteome:
- jPOST: JPST000258
- concentration: 25, 50, 100 mg/kg/day
- exposure: 7 days
- timepoints: after 7 days
- metabolome:
- concentration: 25, 50, 100mg/kg/day
- exposure: 7 days
- timepoints: after 7 days
- metabolites: 88
- concentration: 25, 50, 100mg/kg/day