RNA-seq of isogenic panel of HAP1 cell lines knockout for chromatin remodeling encoding genes
RNA-seq of isogenic panel of HAP1 cell lines knockout for chromatin remodeling encoding genes
HAP1 parental and KO cell lines (RRID:CVCL_Y019) for ARID1A, ARID1B, ARID2, PBRM1, SMARCA2, SMARCA4, KMT2C, KMT2D, CREBBP or SETD2 were purchased from Horizon Discovery. HAP-1 KO cell lines for SMARCB1, BAP-1 or EED were obtained from Drs. Raphaël Margueron (Institut Curie, UMR934, Paris) and Eric Pasmant's teams (Institut Cochin, Paris).  HAP-1 cells were cultured in Iscove's Modified Dulbecco's Medium (IMDM, Gibco) supplemented with 10% FBS (Sigma), 1% Penicillin-Streptomycin (Gibco), 1% Sodium Pyruvate (Gibco), 1% Sodium Bicarbonate (Gibco) and 1% Non-Essential Amino Acids (Gibco).  70-80% confluent cells were harvested, and total RNA was extracted using Rneasy Mini Kit (Qiagen, 74104) with DNAse treatment, according to the manufacturer's instructions. Every RNA sample was quantified with a Qubit Fluorometer and evaluated for quality controls using Agilent 2100 Bioanalyzer Instrument (RRID:SCR_018043). After RNA Integrity Number (RIN) quality control, cDNA libraries were generated using the NEBNext Ultra II RNA Library Prep Kit (NEB #E7775) on Bravo Automated Liquid Handling Platform (RRID:SCR_026137). 