characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2024-02-06T00:25:55Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2024-02-06T00:25:55Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA112675820
characteristics.characteristic: External Id
characteristics.text: MCD, Centre de Biologie Integrative (CBI), CNRS, Universite de Toulouse, UT3
characteristics.characteristic: INSDC center name
characteristics.text: 2024-02-06T00:25:55Z
characteristics.characteristic: INSDC first public
characteristics.text: 2024-02-06T00:25:55Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS14673372
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12712:HiC_siCTRL_mOHT
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: U2OS
characteristics.characteristic: cell_line
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: For Hi-C: 10x106 cells were harvested by trypsin and resuspend in PBS. Formaldehyde was added at a final concentration of 2% and crosslinking was allowed to proceed for 10 min at room temperature. Reaction was stopped by adding Stop solution from Arima Hi-C kit (Arima Genomics) and incubation for 5 minutes at room temperature then incubate for 15 min on ice. Cells were resuspended in PBS and 1x106 cells per aliquot were freeze in liquid nitrogen. DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics, 10% FCS (Invitrogen) with 1 µg/mL puromycin (DIvA cells) at 37°C under a humidified atmosphere with 5% CO2. For AsiSI-dependent DSB induction, cells were treated with 300 nM OHT (Sigma; H7904) for 4h. siRNA transfection were performed using the 4D Nucleofector X (kit SE cell line) according to the manufacturer's instructions and subsequent treatment(s) were performed 48 h later. siRNA: CTRL: siGENOME Non-targeting Control #2 Dharmacon (D-001206-13), siPER2 Dharmacon (M-012977-01) Hi-C experiments were performed in DIvA cells using the Arima Hi-C kit (Arima Genomics) according to the manufacturer’s instructions. 1 million cells were used by condition. Briefly, cells were cross-linked with 2% formaldehyde for 10 min at RT, lysed and chromatin was digested with two different restriction enzymes included in the kit. Ends were filled-in in the presence of biotinylated nucleotides, followed by subsequent ligation. Ligated DNA was sonicated using the Covaris S220 to an average fragment size of 350 bp with the following parameters (Peak incident power: 140; Duty factor: 10%; Cycles per burst: 200; Treatment time: 70s). DNA was then subjected to a double-size selection to retain DNA fragments between 200 and 600 bp using Ampure XP beads (Beckman Coulter). Biotin-ligated DNA was precipitated with streptavidin-coupled magnetic beads (included in the kit). Hi-C library was prepared on beads using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina and NEBNext® Multiplex Oligos for Illumina (New England Biolabs) following instructions from the Arima Hi-C kit.
characteristics.characteristic: description
characteristics.text: osteosarcoma
characteristics.characteristic: disease
characteristics.text: AsiSI-ER
characteristics.characteristic: genotype
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: bone
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: HiC_siCTRL_mOHT
characteristics.characteristic: title