characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2016-05-23T17:06:44Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2016-01-27T15:25:30Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA3857544
characteristics.characteristic: External Id
characteristics.text: Genome-Scale Biology Program, Research Programs Unit and Department of Pathology, Haartman Institute, University of Helsinki
characteristics.characteristic: INSDC center name
characteristics.text: 2016-05-23T17:06:44Z
characteristics.characteristic: INSDC first public
characteristics.text: 2016-01-27T15:25:30Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1044678
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-4356:Balistreri_mIgG_control_0h
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: BC-3
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0002046
characteristics.characteristic: cell line
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: BC-3 cells were grown on RPMI 1640 medium supplemented with 15% FCS (Invitrogen), 100 U/ml penicillin G, and 100 g/ml streptomycin BC-3 cells were cross-linked with 1% formaldehyde in PBS at room temperature for 10min. After a wash in PBS containing 125 mM glycine, cells were collected by centrifugation and sonicated in lysis buffer containing 0,1% SDS, 0,1% sodium deoxycholate, 1 mM EDTA, 10 mM TrisHCl pH 8.0, 140 mM NaCl, 1% Triton X-100 and protease inhibitors to generate chromatin fragments of 100300 bp in length. Following a brief centrifugation (16.000xg, 20 min, 4 C), the fragmented chromatin was immunoprecipitated with a monoclonal antibody against p53 (Clone DO-1, GeneSpin) or control IgG (normal mouse IgG: sc-2025, Santa-Cruz Biotechnology). The precipitates were incubated at 65 C over night to reverse the formaldehyde crosslinking and samples incubated with proteinase K and RNase-A before phenol extraction and ethanol-precipitation of target DNA. Similarly as in Tuupanen et al. Nature Genetics 2009.PMID: 19561604 BC-3 cells were cross-linked with 1% formaldehyde in PBS at room temperature for 10min. After a wash in PBS containing 125 mM glycine, cells were collected by centrifugation and sonicated in lysis buffer containing 0,1% SDS, 0,1% sodium deoxycholate, 1 mM EDTA, 10 mM TrisHCl pH 8.0, 140 mM NaCl, 1% Triton X-100 and protease inhibitors to generate chromatin fragments of 100300 bp in length. Following a brief centrifugation (16.000xg, 20 min, 4 C), the fragmented chromatin was immunoprecipitated with a monoclonal antibody against p53 (Clone DO-1, GeneSpin) or control IgG (normal mouse IgG: sc-2025, Santa-Cruz Biotechnology). The precipitates were incubated at 65 C over night to reverse the formaldehyde crosslinking and samples incubated with proteinase K and RNase-A before phenol extraction and ethanol-precipitation of target DNA. IP-DNA fragments were first repaired using Klenow and T4 DNA polymerases and T4 polynucleotide kinase (MBI Fermentas, Latvia), and then ligated to adapters according to manufacturer's instructions (Illumina). PCR-amplified fragments of approximately 180-300bp were isolated.
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: Balistreri_mIgG_control_0h
characteristics.characteristic: title