characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2018-01-31T17:01:48Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-08-16T18:12:24Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104216897
characteristics.characteristic: External Id
characteristics.text: Toxicogenomics Department Maastricht Universtiy
characteristics.characteristic: INSDC center name
characteristics.text: 2018-01-31T17:01:48Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-08-16T18:12:24Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1875915
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5984:Sample 4
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: mixed pool of Hu8119, Hu1591 and Hu1540 cell lines
characteristics.characteristic: cell line
characteristics.text: hepatocyte
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000182
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: Cryopreserved Primary Human Hepatocytes (PHH, Invitrogen) of 3 individuals (Hu8119, Hu1591 and Hu1540) were thawed for 1 minute at 37°C in a water bath. Next, these PHH were pooled in order to bypass inter-individual variability in susceptibility to toxicants and cultured in 6-well plates in a collagen sandwich, according to the supplier’s protocol (Invitrogen). In brief, 3 vials (one per individual) were thawed in 50mL CHRM medium (CHRM CM7000, Invitrogen) and centrifuged for 10 minutes at 100g at 4ºC. After removing the supernatant, the cell pellet was dissolved in CHPM medium (CHPM CM9000, Invitrogen), which contain FBS, at a concentration of 1.0*10^6 cells/mL. Pooled PHH were cultured in collagen-precoated 24-well plates (Gibco) (density: 0.35*10^6 cells/well) and cells were attached to the wells in the incubator for 4 hours at 37ºC. After the incubation, the debris was removed by shaking and washing the cells twice with William’s medium E (WME CM6000, Invitrogen). Subsequently, cells were covered by 150 µL/well of 1.0mg/mL collagen-mixture (containing 10*DMEM, 1.0mg/mL Collagen type 1 (BD), 0.2M NaOH and, MQ) and incubated at 37°C for approximately 30 minutes until the collagen was fixed. After that, culture medium (WME + 20mL Hepatocyte Supplement Pack (CM4000, Invitrogen) substituted with 1% penicillin/streptomycin (Gibco)) was added. Primary human hepatocytes (PHH) were exposed daily for 3 days to 15 mM VPA after which RNA was isolated. After terminating the VPA treatment, part of the cells were kept with medium for 3 days (washout-period (WO-period)) in order to investigate the eventual persistence of VPA-induced transcriptome changes. Starting from the RNA samples, RNAs were size selected and ligated for sequencing following the TruSeq™ SBS Kit v3 paired-end by sequencing by synthesis (SBS) We have used the Trizol LS Reagent protocol (Life Technologies)
characteristics.characteristic: description
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: organism
characteristics.text: liver
characteristics.characteristic: organism part
characteristics.text: 2
characteristics.characteristic: replicate
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: Sample 4
characteristics.characteristic: title