title: MDCK_Input-WT-rep1
organism: Canis lupus familiaris
description: 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. ChIP-Seq/MNase-Seq libraries were constructed using NEBnext Ultra DNA Library Prep kit for Illumina (New England Biolabs).
attributes.tag: ENA first public
attributes.value: 2017-10-23
attributes.tag: ENA last update
attributes.value: 2017-04-04
attributes.tag: External Id
attributes.value: SAMEA103957219
attributes.tag: INSDC center alias
attributes.value: Research Fellow Tremethick Lab Department of Genome Sciences The John Curtin School of Medical Research The Australian National University
attributes.tag: INSDC center name
attributes.value: Research Fellow Tremethick Lab Department of Genome Sciences The John Curtin School of Medical Research The Australian National University
attributes.tag: INSDC first public
attributes.value: 2017-10-23T17:03:32Z
attributes.tag: INSDC last update
attributes.value: 2017-04-04T14:24:03Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-5637:MDCK_Input-WT-rep1
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell line
attributes.value: MDCK
attributes.tag: cell type
attributes.value: Epithelial cell of kidney
attributes.tag: common name
attributes.value: dog
attributes.tag: organism part
attributes.value: kidney
attributes.tag: sample name
attributes.value: E-MTAB-5637:MDCK_Input-WT-rep1
attributes.tag: sex
attributes.value: female
attributes.tag: sub_species
attributes.value: familiaris