characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2014-04-03T17:00:38Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T17:07:58Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2335253
characteristics.characteristic: External Id
characteristics.text: ERASMUSMC
characteristics.characteristic: INSDC center name
characteristics.text: 2014-04-03T17:00:38Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T17:07:58Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS393447
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-2224:MOLM1_INPUT_H3K4ME1
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: MOLM-1
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0006652
characteristics.characteristic: cell line
characteristics.text: myeloblast
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000835
characteristics.characteristic: cell type
characteristics.text: 3q-aberration
characteristics.characteristic: chromosome aberration
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: Cell lines were cultured using media conditions as follows. MUTZ-3: 60% alpha-MEM (Life Technologies), 20% FBS (PAA), 20% conditioned medium of cell line 5637, and 10 ng/ml hrGM-CSF (Amgen); K562, MOLM-1, and U937: 90% RPMI and 10% FBS. All cultures contained 50 U/ml penicillin and 50 μg/ml streptomycin (Sigma). JQ1 sensitivity was measured by mitochondrial dehydrogenase (MTT assay) after 6, 24, 48, and 72 h of exposure with JQ1 (5, 50, 500, or 1,000 nM) or vehicle control (DMSO, 0.05%). The cell line MOLM1 was treated for 6 hours with 1,000 nM of JQ1. Subsequently, a BRD4 Chip-Seq was performed on these cells to determine the effect of JQ1 treatment of enhancers and super enhancers. Immunoprecipitated material was de-crosslinked and was amplified using a Whole Genome Amplification kit (WGA2/WGA3; Sigma-Aldrich, Zwijndrecht, The Netherlands). Subsequently, the fragments were sheared by a Covaris shearing device (Covaris S2) and size selected by an agrose gel. ChIP experiments were performed as previously described (Bindels et al., 2012; doi: http://dx.doi.org/10.1182/blood-2011-11-393827). Immunoprecipitation of cross-linked chromatin was performed with antibodies directed against Histone H3K4me1, H3K4me3, H3K27ac, p300, and BRD4, or an equal amount of isotype IgG as background control. Three independent experiments were performed and the amount of immunoprecipitated DNA was represented relative to cross-linked input DNA.
characteristics.characteristic: description
characteristics.text: wild type
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005168
characteristics.characteristic: genotype
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: frozen specimen
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/OBI_0000922
characteristics.characteristic: specimen with known storage state
characteristics.text: MOLM1_INPUT_H3K4ME1
characteristics.characteristic: title