characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2018-03-01T17:01:49Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-09-04T10:29:58Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104279661
characteristics.characteristic: External Id
characteristics.text: Pulmonary and Critical Care Medicine, Stanford University School of Medicine
characteristics.characteristic: INSDC center name
characteristics.text: 2018-03-01T17:01:49Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-09-04T10:29:58Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1904639
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-6042:NF90_K562_ChIPSeq
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: K562
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0002067
characteristics.characteristic: cell line
characteristics.text: lymphoblast
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000572
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: Cells were harvested and crosslinked in 1% formaldehyde for 10 minutes at room temperature. Cell pellets were re-suspended in hypotonic buffer (20 mM HEPES, 10 mM KCl, 1mM EDTA, 10% glycerol) supplemented with Pierce Protease Inhibitor Tablets (Thermo Fisher), placed on ice for 10 minutes and centrifuged to remove cytoplasmic supernatant. Chromatin was released from nuclear pellet with mild chemical lysis with Radio-immunoprecipitation assay buffer (RIPA) containing 0.1% SDS and 1% Triton-X-100. Protein-bound chromatin was sheared with mechanical sonication (Branson 250 Sonifier) at 35% output with 20 second pulses for 30 cycles to obtain chromatin fragments of high resolution at 200 â€“ 500 bps. Successful chromatin fragmentation was assayed by reverse cross-linking, and electrophoresis through 0.8% agarose gel to confirm enrichment of small chromatin fragments at the target range. K562 erythroleukemia cells were grown in RPMI1640 media supplemented with 10% fetal bovine serum and Antibiotic-Antimycolic 100X (Life Technologies). Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with with monoclonal antibody to NF90 (BD mAB DRBP76 #612155). Libraries were prepared according to Bravo automatic library preparation.
characteristics.characteristic: description
characteristics.text: chronic myelogenous leukemia
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000339
characteristics.characteristic: disease
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: bone marrow
characteristics.characteristic: organism part
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: NF90_K562_ChIPSeq
characteristics.characteristic: title