characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2017-10-23T17:03:32Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-04-04T14:24:03Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA103957215
characteristics.characteristic: External Id
characteristics.text: Research Fellow Tremethick Lab Department of Genome Sciences The John Curtin School of Medical Research The Australian National University
characteristics.characteristic: INSDC center name
characteristics.text: 2017-10-23T17:03:32Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-04-04T14:24:03Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1646383
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5637:MDCK_H2AZ-WT-rep1
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: MDCK
characteristics.characteristic: cell line
characteristics.text: Epithelial cell of kidney
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0002518
characteristics.characteristic: cell type
characteristics.text: dog
characteristics.characteristic: common name
characteristics.text: Protocols: MDCK cells were maintained in DMEM growth medium supplemented with 10% Foetal Bovine Serum (FBS) Nuclei were pelleted by centrifugation for 40 min at 4,000g through an 8-ml sucrose cushion (1.2 M sucrose, 60 mM KCL, 15 mM HEPES, 15 mM NaCl, 2 mM MgCl2, 1 mM EDTA, 0.5 mM EGTA, 0.5 mM DTT, 0.2 mM PMSF and protease inhibitor cocktail, pH 7.6). The supernatant was carefully removed, and pelleted nuclei were resuspended in 1 ml of micrococcal digestion buffer (50 mM Tris-HCl pH 7.6, 3 mM CaCl2) and passed five or six times through a size 29-gauge needle. The nuclear extract was digested for 35 min at 37 °C with micrococcal nuclease (New England Biolabs; 40 gel units per 330 μl of extract) to obtain ~80% mononucleosomes. After centrifugation at 10,000g for 5 min, the supernatant (S1) and the resuspended pellet (S2) were dialyzed against 10 mM Tris-HCl pH 7.6, 1 mM EDTA and 0.5 mM EGTA overnight at 4 °C. The S1 and S2 supernatants were then combined and dialyzed against 10 mM Tris-HCl pH 7.6, 1 mM EDTA, 0.5 mM EGTA, 4% (v/v) glycerol, divided into aliquots and stored at −80 °C. For ChIP, 5 ug of anti- H2A.Z antibodies were used for 150 uq of MNAse digested chromatin. Samples were then RNAse treated for 30 mins at 37 degrees followed by Proteinase K at 65 degrees for 5 hours to decrosslink and release DNA. Finally, AMPure beads were used to purify the ChIP/Input DNA. ChIP-Seq/MNase-Seq libraries were constructed using NEBnext Ultra DNA Library Prep kit for Illumina (New England Biolabs).
characteristics.characteristic: description
characteristics.text: Canis lupus familiaris
characteristics.characteristic: organism
characteristics.text: Canis lupus familiaris
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9615
characteristics.characteristic: organism
characteristics.text: kidney
characteristics.characteristic: organism part
characteristics.text: Canis lupus familiaris
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000383
characteristics.characteristic: sex
characteristics.text: MDCK_H2AZ-WT-rep1
characteristics.characteristic: title