characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2015-06-30T17:01:04Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T18:16:13Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2730815
characteristics.characteristic: External Id
characteristics.text: Systems Biology Ireland, University College Dublin now: European Molecular Biology Laboratory
characteristics.characteristic: INSDC center name
characteristics.text: 2015-06-30T17:01:04Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T18:16:13Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS487268
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-2689:24h_RA_A
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: SH-SY5Y/6TR(EU)/pTrex-Dest-30/MYCN
characteristics.characteristic: cell line
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: Total mRNA was extracted using TRI Reagent (Sigma-Aldrich) according to manufacturers protocol and DNA was digested with DNA-free Kit (Applied Biosystems). RNA quality was checked by RT-qPCR (as above) and on a 2100 Bioanalyser (Agilent) using a Eukaryote Total RNA Nano Chip (version 2.6). All samples had a RIN value in the range of 9.8-10. Sequencing libraries were generated from 2ug of total RNA per sample with TruSeq RNA sample preparation Kit v2 (Illumina) according to manufacturers protocol. Size and purity of the libraries were analysed on a Bioanalyser High Sensitivity DNA chip (Agilent). Libraries were clustered using TruSeq Single-End Cluster Kit v5-CS-GA (Illumina). Cells were cultured in RPMI 1640 (Gibco), supplemented with 10% fetal bovine serum (FBS) (Gibco), 2mM L-glutamine (Gibco) and 1% Penicillin-Streptomycin solution (Gibco) Azak was dissolved in DMSO in order to apply it to the cells. Therefore a vehicle control consisting of SY5Y-MYCN cells treated with 24h 1µl/ml DMSO only was used in duplicates. Doxycycline (Sigma) dissolved in water was used at a final concentration of 1μg/ml to induce MYCN expression in SY5Y-MYCN. A co-treatment study with Dox and Azak was conducted. SY5Y-MYCN cells were treated with 24h Azak, 24h Azak & 48h Dox and 48h Dox, with biological duplicates. 1 μM RA (dissolved in DMSO) and 1 μg/mL Doxycycline were given individually and in combination. SY5Y-MYCN cells were treated with 24h RA, 24h RA & 48h Dox, and 48h Dox and RNA was extracted in biological duplicates. For the 24h RA & 48h Dox co-treatment cells were treated with Dox for 24h and then with RA and fresh Dox for a further 24h. mRNA was extracted using TRI Reagent (Sigma-Aldrich) according to manufacturers protocol
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: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: 24h_RA_A
characteristics.characteristic: title