CRC cell lines (LS174T, T84, LS180, HCT15, HT29, SW620, COLO205, HCT116, COLO320, LoVo, CaCo2) were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA) and grown in media with supplements as described in Additional file 1 : Table S2 under humidified atmosphere of 5% CO2.
Treatment with DNA methyltransferase inhibitor (DNMTi): 3.5 × 104 COLO205 or SW620 cells were seeded in six-well plates and treated with 0.5% DMSO, 1.25 μM, 2.5 μM, 5 μM, and 10 μM of decitabine (Stock 50 mM in DMSO, Cat.#S1200, Selleckchem, Houston, TX, USA) for 48 h.
Treatment with histone deacetylase inhibitors (HDACi): 3.5 × 104 COLO205 or SW620 cells were seeded in six-well plates and treated with 0.01% DMSO, 50 nM trichostatin A (Stock 5 mM in DMSO, Cat.# T8552, Sigma-Aldrich, St. Louis, MO, USA) and 20 nM LMK-235 (Stock 10 mM in DMSO, Cat.# S7569, Selleckchem) alone or in combination with 2.5 μM, 5 μM, and 10 μM of decitabine for 48 h.
3.5 × 104 HT29, SW620, LS174T, and LoVo cells were seeded in six-well plates and treated with 8 × 10−3 DMSO, 5 nM, 10 nM, 20 nM, 40 nM, and 80 nM of LMK-235 for 48 h.
Treatment with DNA methyltransferase inhibitor (DNMTi): 3.5 × 104 COLO205 or SW620 cells were seeded in six-well plates and treated with 0.5% DMSO, 1.25 μM, 2.5 μM, 5 μM, and 10 μM of decitabine (Stock 50 mM in DMSO, Cat.#S1200, Selleckchem, Houston, TX, USA) for 48 h.
Treatment with histone deacetylase inhibitors (HDACi): 3.5 × 104 COLO205 or SW620 cells were seeded in six-well plates and treated with 0.01% DMSO, 50 nM trichostatin A (Stock 5 mM in DMSO, Cat.# T8552, Sigma-Aldrich, St. Louis, MO, USA) and 20 nM LMK-235 (Stock 10 mM in DMSO, Cat.# S7569, Selleckchem) alone or in combination with 2.5 μM, 5 μM, and 10 μM of decitabine for 48 h.
3.5 × 104 HT29, SW620, LS174T, and LoVo cells were seeded in six-well plates and treated with 8 × 10−3 DMSO, 5 nM, 10 nM, 20 nM, 40 nM, and 80 nM of LMK-235 for 48 h.