characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2016-06-27T11:01:18Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T18:52:56Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2625909
characteristics.characteristic: External Id
characteristics.text: University of Manchester
characteristics.characteristic: INSDC center name
characteristics.text: 2016-06-27T11:01:18Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T18:52:56Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS496031
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-2701:IgG_control_R1
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: U2OS
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0002869
characteristics.characteristic: cell line
characteristics.text: osteosarcoma
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000637
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: After reverse cross-link and protein digestion with Proteinase K (Roche), DNA was purified using Qiaquick, PCR purification kit (Qiagen) following the manufacturer's instructions. The stable cell lines were grown in DMEM supplement with 10% foetal bovine serum. Media contained 100 micro-g/ml of Hygromycin. Expression of ZMYM2(WT) or ZMYM2(SIM2mut) was induced by treating the cells for 48 hours with 100 ng/ml [for ZMYM2(WT)] or 50 ng/ml [for ZMYM2(SIM2mut)] doxycycline (Sigma). Expression of FOXO3 was induced by treating the cells for 48 hours with 1 ng/ml doxycycline (Sigma). Cells were double cross-linked with dimethyl adipimidate (DMA) for 20 minutes and subsequently with Formaldehyde for 10 minutes. ChIP-seq was performed as described in Schmidt et al., 2009, using 60 x 106 U2OS-ZMYM2(WT) or U2OS-ZMYM2(SIM2mut). Immuno-precipitation was performed overnight at 4 degrees C by incubating the shared DNA-protein complex with 6 ug of anti-Flag (Sigma) or control IgG (Millipore) antibodies previously coupled to Dynabeads protein G (Invitrogen). Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. (2009) ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48: 240-248. Note: paired-end sequencing libraires were created in this experiment but only the forward (R1) reads are available in this submission. The 'LIBRARY_LAYOUT' attribute is therefore set to be 'SINGLE' rather than 'PAIRED'.
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: female
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000383
characteristics.characteristic: sex
characteristics.text: IgG_control_R1
characteristics.characteristic: title