characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2015-02-07T17:01:22Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T22:59:07Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA3182862
characteristics.characteristic: External Id
characteristics.text: Max-Delbruck-Centrum Berlin
characteristics.characteristic: INSDC center name
characteristics.text: 2015-02-07T17:01:22Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T22:59:07Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS636046
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-3140:H3K4me3_Salt_2
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: macrophage
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000235
characteristics.characteristic: cell type
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Primary bone-marrow-derived murine macrophages were grown in RPMI1640 (GIBCO) supplemented with 10% FCS, 10mM HEPES, 1% Penicillin-Streptomycin, 5uM beta-mercaptoethanol at a density of 40 million cells per 150cm(2) cell culture flask. After attachment for 2h cells were stimulated with 10ng/ml LPS (Sigma-Aldrich) [M(LPS)] or 10ng/ml IL-4 (R&D Systems) and 10ng/ml IL-13 (Invitrogen) for 24h. 40mM NaCl were added where applicable. 40 million macrophages per group were used to isolate nuclei by centrifugation through a dense sucrose cushion. Subsequently, samples were digested with micrococcal nuclease (Sigma-Aldrich) to generate native chromatin templates consisting mainly of mononucleosomes. Abundance of mononucleosomal DNA was confirmed by gel electrophoresis. Chromatin was extracted with RIPA buffer and cellular debris removed by centrifugation. Subsequently, chromatin was precipitated over night at 4C with anti-H3K4me3 (NEB #9751 S) or anti-H4Ac (Millipore #06-866) bound to Dynabeads Protein A (Invitrogen #10002D). MinElute PCR Purification Kit (QIAGEN) was used to purify immunoprecipitated DNA after Proteinase K (Sigma-Aldrich) digestion at 65C for 4h. 50ng of purified DNA was used for library preparation with the TruSeq ChIP sample preparation kit (Illumina) according to the manufacturer's instructions.
characteristics.characteristic: description
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_10090
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: C57BL/6JOlaHsd
characteristics.characteristic: strain
characteristics.text: H3K4me3_Salt_2
characteristics.characteristic: title