ARID1A Depletion in mESCs

All cell lines used in this study originate from E14TG2a.4 mESC (mouse Embryonic Stem Cells, Mus musculus strain 129/Ola, male) with integrated gene targeting vector pAW2 at the ROSA26 locus to enable recombinase-mediated cassette exchange (Zhou et al., 2013 (link)). mESC cells were grown in G-MEM medium (ThermoFisher) supplemented with 5% embryonic stem cell-qualified FBS (ThermoFisher), 5% Knockout Serum Replacement (ThermoFisher), 1x non-essential amino acids (ThermoFisher), 1x sodium pyruvate (ThermoFisher), 100 μM β-mercaptoethanol (Sigma-Aldrich) and 1000 U/mL LIF (Millipore). Cells were sub-cultured every two days into dishes coated with 0.1% gelatine and kept at 37°C in a 5% CO₂ water-saturated incubator.
For depletion of ARID1A, cells were seeded at ∼20,000 cells per cm² and 500 μM auxin analog 1-naphthaleneacetic acid (NAA, Sigma-Aldrich) in 1M sodium hydroxide was added for the indicated time before harvesting the cells after two days of growing.