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:
    • Tuomela et al. (2013)
    • pubmed ID: 23894303
    • NCBI GEO: GSE39316
    • tissue: human monocyte-derived macrophages (HMDM)
    • concentration: 1000ng/ml, 10000ng/ml
    • timepoints: 6h, 24h of exposure
  • 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:
    • Fede et al. (2014)
    • pubmed ID: 25170680
    • NCBI GEO: GSE53700
    • tissue: human lung adeoncarcinoma A549
    • particle size: 9nm (SM30), 18nm (AS30)
    • concentration: 0.6mg/ml
    • treatment: 2h
    • post treatment recovery: 3h, 22h
  • 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