Effects of culture conditions on epigenomic profiles of brain tumor cells

We performed epigenomic analysis of brain tumor cells that were collected from micro-engineered three-dimensional tumor models. We used a low-input epigenomic analysis method known as microfluidic-oscillatory-washing-based chromatin immunoprecipitation with sequencing (MOWChIP-seq) to analyze genome-wide histone modification (H3K4me3). We compared H3K4me3 patterns in standard 2D cultures and 3D cultures based on type I collagen hydrogels, under both normoxic and hypoxic conditions. Our work illustrates a direct connection between cell culture or tissue niche condition and genome-wide alterations in histone modification. We obtained genome-wide H3K4me3 profiles in U251 cells cultured under different conditions (3D vs. 2D, Hypoxia vs. Normoxia). The MOWChIP-seq experiments were performed using 1000 cells per assay as described in our previous publication (Cao et al. Nature Methods 12 (2015) 959-962). We generated two replicates (R1 and R2) for each sample.