characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2014-04-30T17:00:36Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T16:38:13Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2168811
characteristics.characteristic: External Id
characteristics.text: Department of Immunology, Genetics and Pathology, Genomics, Uppsala University
characteristics.characteristic: INSDC center name
characteristics.text: 2014-04-30T17:00:36Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T16:38:13Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS337415
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-1750:hepg2_trt
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: HepG2
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001187
characteristics.characteristic: cell line
characteristics.text: hepatocellular carcinoma
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000182
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: HepG2 cells were cultured to confluence in RPMI 1640 medium supplemented with 10% FBS. Cells were serum-starved over night (1 % FBS) before stimulation with TGF-b1 (final conc. 2.5 ng/ml in complete medium). TGF-b1 treated and control cells were harvested after 1 hour treatment. HepG2 cells were cultured in RPMI 1640 medium with 10% FBS .Cells were serum starved over night with 1% FBS containing medium and treated the cells with 2.5ng/ml (final vomv) of TGFB1.for 1 hour. The cells were washed with PBS and resuspended in ice cold buffer A (0.32M sucrose, 15 mM Hepes pH 7.9, 60Mm KCl , 2 mM EDTA, 0.5 mM EGTA, 0,5 % Bovine serum albumin , 0.5 mM spermidine, 0.15 mM spermine and 0.5 mM DTT). After a short incubation on ice, cells were homogenized with a Dounce homogenizer. The nuclear suspension was slowly layered on an equal volume of ice cold buffer B (30% sucrose, 15 mM Hepes pH 7.9, 60 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.15 mM spermine and 0.5 mM DTT) and centrifuged at 3000 rpm for 15 minutes to pellet the nuclei. Collected nuclei were washed once and resuspended in buffer N (0.34 mM sucrose, 15 mM HEPES pH 7.5, 60 mM KCl, 15 mM NaCl, 0.5 mM spermidine, 0.15 mM spermine, and 0.15 mM beta-mercaptoethanol). Samples were adjusted to 3 mM CaCl2 and the nuclear suspension was adjusted to 30 million cells per milliliter and incubated at 37 degrees C for 5 minutes. Micrococcal nuclease (MNase, 300U) was added to each aliquot and incubated for another 5 minutes at 37 degrees C. Buffer S, containing 90 mM HEPES pH 7.9, 220 mM NaCl, 10 mM EDTA, 2% Triton X-100, 0.2% Na-deoxycholate, 0.2%SDS, 0.5 mM PMSF, and 2 ug/ml aprotinin was added to stop the reaction. The solution was centrifuged and the supernatant was used to extract the DNA by Phenol/chloroform/ethanol precipitation. DNA was loaded on 2% agarose gel and the mononucleosome size DNA (147 bp) fragments were excised. Excised gel fragments were purified by using a Quiagen gel extraction kit. Libraries of nucleosomal DNA were prepared according to the SOLiD fragment library protocol and sequenced using v3 chemistry.
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: male
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000384
characteristics.characteristic: sex
characteristics.text: hepg2_trt
characteristics.characteristic: title