characteristics: ERC000011
characteristics: ENA-CHECKLIST
characteristics: 2022-09-30T00:20:53Z
characteristics: ENA-FIRST-PUBLIC
characteristics: 2022-09-30T00:20:53Z
characteristics: ENA-LAST-UPDATE
characteristics: SAMEA110590504
characteristics: External Id
characteristics: Wallenberg Center for Molecular Medicine (WCMM) Department of Biomedical and Clinical Sciences (BKV) Division of Molecular Medicine and Virology (MMV) Faculty of Medicine and Health Sciences, Linkoping University, Linkoping, Sweden
characteristics: INSDC center name
characteristics: 2022-09-30T00:20:53Z
characteristics: INSDC first public
characteristics: 2022-09-30T00:20:53Z
characteristics: INSDC last update
characteristics: public
characteristics: INSDC status
characteristics: ERS12688279
characteristics: SRA accession
characteristics: E-MTAB-12076:hESC_CHIR_24h_B
characteristics: Submitter Id
characteristics: ArrayExpress
characteristics: broker name
characteristics: hESC
characteristics: cell_line
characteristics: embryonic stem cell
characteristics: cell_type
characteristics: human
characteristics: common name
characteristics: Protocols: Cells collected from cell cultures, see growth protocol. HEK293T cells (HEK293Ts) were cultured in medium consisting of DMEM, high glucose (41966-029, Gibco - Thermo Fisher Scientific) supplemented with 10% Calf Bovine Serum (12133C, Sigma-Aldrich) and 10 U/ml Penicillin-Streptomycin (15276355, Gibco - Thermo Fisher Scientific). HEK293Ts were passaged by incubation in Trypsin EDTA 0.25% (25-200-056, Thermo Fisher Scientific). hESCs were cultured in Essential 8TM medium (A1517001, ThermoFisher Scientific) in plates and flasks coated with 10 mg/ml Vitronectin (A14700, ThermoFisher Scientific). Cells were passaged by incubation in 0.5 mM EDTA-PBS (stock: 0.5 M EDTA, AM9260G, Thermo Fisher Scientific). Both cell types were treated with 10 mM CHIR99021 for 4 hours, 24 hours and 3 days (n = 3 samples for each condition). Cells were collected, lysed in ice cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), and pelleted. Pelleted nuclei were incubated in 50 ml transposition reaction mix (20034210, Illumina) at 370C for 30 minutes. Transposed DNA fragments were amplified for 13 cycles in the presence of Custom Nextera PCR primers (Buenrostro et al., 2013) using the NEBNext High-Fidelity 2x PCR Master Mix (Cat. #M0541, New England Biolabs). Libraries were purified using the High Pure PCR Production Purification Kit (11732676001, Roche / Sigma-Aldrich). Libraries were validated on an Agilent 2100 and quantified using quantitative PCR (Q-PCR).
characteristics: description
characteristics: embryo stage
characteristics: developmental stage
characteristics: normal
characteristics: disease
characteristics: wild type genotype
characteristics: genotype
characteristics: Homo sapiens
characteristics: organism
characteristics: Homo sapiens
characteristics: organism
characteristics: inner cell mass
characteristics: organism part
characteristics: 2
characteristics: replicate
characteristics: Homo sapiens
characteristics: scientific_name
characteristics: hESC_CHIR_24h_B
characteristics: title