EXPERIMENT_TITLE: Illumina NovaSeq 6000 paired end sequencing; HiC data of the human oesophageal adenocarcinoma (EAC) cell lines OE19
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: 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.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: This dataset consists of in situ HiC-seq data from a human oesophageal adenocarcinoma cell line (OE19). In total, the dataset includes 2 biological replicated samples. The Hi-C sample and library preparations were generated using Arima-HiC Kit (A510008, ARIMA Genomics) and Arima Library Prep module (A303011, ARIMA Genomics), respectively.
SAMPLE_TITLE: OE19_HiC_rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "ENA-FIRST-PUBLIC", "VALUE": "2023-02-21"}, {"TAG": "ENA-LAST-UPDATE", "VALUE": "2023-02-21"}, {"TAG": "External Id", "VALUE": "SAMEA112653957"}, {"TAG": "INSDC center alias", "VALUE": "Faculty of Biology, Medicine and Health, University of Manchester"}, {"TAG": "INSDC center name", "VALUE": "Faculty of Biology, Medicine and Health, University of Manchester"}, {"TAG": "INSDC first public", "VALUE": "2023-02-21T10:22:10Z"}, {"TAG": "INSDC last update", "VALUE": "2023-02-21T10:22:10Z"}, {"TAG": "INSDC status", "VALUE": "public"}, {"TAG": "Submitter Id", "VALUE": "E-MTAB-12664:OE19_HiC_rep1"}, {"TAG": "age", "VALUE": "72"}, {"TAG": "broker name", "VALUE": "ArrayExpress"}, {"TAG": "cell_line", "VALUE": "OE19"}, {"TAG": "cell_type", "VALUE": "epithelial cell"}, {"TAG": "common name", "VALUE": "human"}, {"TAG": "developmental stage", "VALUE": "adult"}, {"TAG": "disease", "VALUE": "esophageal adenocarcinoma"}, {"TAG": "organism part", "VALUE": "esophagus"}, {"TAG": "replicate", "VALUE": "1"}, {"TAG": "sample name", "VALUE": "E-MTAB-12664:OE19_HiC_rep1"}, {"TAG": "scientific_name", "VALUE": "Homo sapiens"}, {"TAG": "sex", "VALUE": "male"}]
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