title: OE19_HiC_rep1
organism: Homo sapiens
description: Protocols: OE19 cells were cultured in RPMI 1640 (ThermoFisher Scientific, 52400) supplemented with 10% foetal bovine serum (ThermoFisher Scientific, 10270). For biological replicates, cells were trypsineised and fixed in PBS containing 2% fresh formaldehyde and quenched with stop solution 1 as manufactured described (A510008, ARIMA Genomics). Cell pellets were stored at -80째C. The nuclei were prepared from 3 million cross-linked cell pellets (-80째C) using Nuclei EZ prep kit (NUC101, Sigma-Aldrich), followed by chromatin digestion with a cocktail of restriction enzymes,biotinylation, proximal ligation, proteinase K treatment and reverse crosslink, Ampure XP DNA purification, sonication (COVARIS S220) Ampure XP size selection and biotin T1 beads pull-down as manufactured described (A510008, ARIMA Genomics). HiC libraries were generated using Arima Library Prep module (A303011, ARIMA Genomics) as manufactured described. Briefly, pulled-down DNA was end-repaired and adapters ligated. The material was PCR amplified for 5 cycles.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2023-02-21
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2023-02-21
attributes.tag: External Id
attributes.value: SAMEA112653957
attributes.tag: INSDC center alias
attributes.value: Faculty of Biology, Medicine and Health, University of Manchester
attributes.tag: INSDC center name
attributes.value: Faculty of Biology, Medicine and Health, University of Manchester
attributes.tag: INSDC first public
attributes.value: 2023-02-21T10:22:10Z
attributes.tag: INSDC last update
attributes.value: 2023-02-21T10:22:10Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-12664:OE19_HiC_rep1
attributes.tag: age
attributes.value: 72
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell_line
attributes.value: OE19
attributes.tag: cell_type
attributes.value: epithelial cell
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: disease
attributes.value: esophageal adenocarcinoma
attributes.tag: organism part
attributes.value: esophagus
attributes.tag: replicate
attributes.value: 1
attributes.tag: sample name
attributes.value: E-MTAB-12664:OE19_HiC_rep1
attributes.tag: scientific_name
attributes.value: Homo sapiens
attributes.tag: sex
attributes.value: male