Epigenomic profiling of EWS-FLI1-regulated genes

A673 cells were cultured as previously described (Carrillo et al., 2007 (link)). DNA, chromatin, RNA, and protein were collected following standard procedures from untreated cells (EWS-FLI1-high state) and 53 hr after adding doxycycline to the media (EWS-FLI1-low state). To assess DNA methylation, WGBS and RRBS experiments were performed using custom protocols (see the Supplemental Experimental Procedures for details), and the data of both assays were merged. ChIP-seq experiments were performed using the iDeal ChIP-seq kit (Diagenode) according to manufacturer instructions. ATAC-seq was performed as previously described (Buenrostro et al., 2013 (link)) with minor adaptations for A673 cells. RNA-seq used Illumina kits for strand-specific library preparation. All sequencing was performed by the Biomedical Sequencing Facility at CeMM using Illumina HiSeq 2000 sequencers.
The epigenome maps as well as the raw and processed data underlying the presented analyses are available online at http://tomazou2015.computational-epigenetics.org.