characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2017-12-31T17:01:44Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-08-31T10:25:37Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104233036
characteristics.characteristic: External Id
characteristics.text: Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, and Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University
characteristics.characteristic: INSDC center name
characteristics.text: 2017-12-31T17:01:44Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-08-31T10:25:37Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1892054
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-6032:Sample 4
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 fixed in 1% formaldehyde for 8 min at room temperature. Nuclei were isolated using Lysis Buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40), transferred to Sonication Buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM EGTA, 4 mM EDTA, 0.1% SDS, 1% Triton X-100, 1% NP-40) and sonicated (Bioruptor, Diagenode) for 30 cycles of 30 sec on / 30 sec off at high intensity. Each immunoprecipitation (IP) was carried out on the equivalent of 50 x 106 cells in IP Buffer (150 mM NaCl, 50 mM Tris-HCl pH 7.5, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100) overnight at 4°C. The antibody slurry was prepared with 50 µl A-, 50 µl G-Dynabeads and 60 µg.ml-1 antibody per IP. See; Herdman et al. (2017). PLoS Genetics 13, e1006899. Rabbit polyclonal antibodies against mouse UBF, RPI large subunit (RPA194/Polr1A)were generated in the laboratory. Anti-RPA194 (#5) and anti-UBF (#8) antisera were raised against mouse RPA194 (aa 231-429) and mouse UBF (aa 2-404) ref: https://doi.org/10.1016/j.molcel.2010.03.015. K562 cells were grown to subconfluence in Iscove's Modified Dulbecco's Medium, 10% fetal bovine serum. Immunoprecipitated chromatin was treated with RNaseA and the DNA isolated using 2% Na SDS and 2mg.ml-1 Proteinase-K. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end sequencing on an Illumina HiSeq 2000 (McGill University and Genome Qubec Innovation Centre).
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: Sample 4
characteristics.characteristic: title