characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-03-21T00:17:49Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-03-21T00:17:49Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA112648449
characteristics.characteristic: External Id
characteristics.text: Department of Biochemistry, University of Oxford, Oxford, UK Instituto Gulbenkian de Ciencia, Oeiras, Portugal
characteristics.characteristic: INSDC center name
characteristics.text: 2023-03-21T00:17:49Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-03-21T00:17:49Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS14646170
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12624:ATAC_Primed3h
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: HeLa
characteristics.characteristic: cell_line
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: The ATAC-seq procedure was adapted from Omni-ATAC protocol (Corces et al. 2017). Briefly, 50,000 naive or primed cells treated with IFNγ for 1h and 3h and non-treated cells were centrifuged for 5 minutes at 500g, resuspended in 50μL of cold ATAC lysis buffer (10mM Tris-HCl pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% NP-40; 0.1% Tween-20 and 0.01% Digitonin), and incubated on ice for 3 minutes. Next, 1mL wash buffer was added to the pellets (10mM Tris-HCl pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% Tween-20), cells were resuspended and immediately centrifuged for 10 minutes at 500g at 4°C. Next cell pellets were resuspended in 50μL tagmentation reaction buffer [25μL 2 × TD buffer, 16.5μL 1X PBS, 0.1% Tween-20, 0.01% Digitonin, 5.4μL nuclease-free water and 2.5μL TDE1 (Tn5 enzyme, Illumina)] followed by incubation at 37°C for 30 minutes. All cell lines were incubated at 37oC, 5% CO2, and grown in 'Dulbecco's Modified Eagle Medium (DMEM) containing high glucose and pyruvate (ThermoFisher, 41966-029) supplemented with 10% NCS (newborn calf serum, ThermoFisher, 16010-159) and 1% Penicillin-Streptomycin (ThermoFisher, 15140-122). HeLa cells which primed with IFNγ for 24 hours, followed with IFNγ washout. After 48h, naïve and primed cells were induced by IFNγ for 1h and 3h. DNA was then purified using MinElute PCR Purification Kit (QIAGEN) (10μL elution). the purified DNA was amplified by Q5 Hot start DNA polymerase using described indexing primers (Buenrostro et al. 2013). The thermal cycling process was programmed as follows: 72°C for 5 minutes and 98°C for 30s, and five cycles of (98°C 10s; 63°C 30s; 72°C 1 minute); followed by subsequent library quantification using qPCR with the following program: 95°C for 30s, 95°C for 10s, 58°C for 30s, 72°C for 1 minute, and additional PCR amplification that is needed for each sample to reach 1/3 of saturated signal. DNA library was purified and size selected using a double-sided bead purification protocol with AMPure XP beads that removes both unwanted small and large fragments (Beckman Coulter). The QuBit dsDNA HS Assay (Thermo Fisher Scientific) was used to determine DNA concentration according to the 'manufacturer's protocol. Fragment size was estimated by DNA TapeStation (Agilent High Sensitivity D1000) prior to mixing of multiplexed libraries diluted to 2nM concentration (calculated based the on Qubit dsDNA HS Assay Kit)
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: adenocarcinoma
characteristics.characteristic: disease
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: uterine cervix
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: ATAC_Primed3h
characteristics.characteristic: title