ChIP-seq data processing

Regions of enrichment (peaks) were identified using EDD version 1.0.2 (Lund et al. 2014) and SICER version 1.1 (Zang et al. 2009). Since EDD's auto parameter estimation was unsuited for our data sets, we used the parameter set “-b 11 –g 5 –fdr 0.1” (bin size 11 kb, gap penalty 5) suggested for lamin A by Lund et al. (2014). Based on visual inspection, these settings yielded the best results for our data. For SICER, we used a window size of 1000 bp, a gap size of 3000 bp, and a false discovery rate of 0.01, to account for the characteristics of lamin and LAP2alpha binding. See Supplemental Material for more details and Table 1 for information on peak number and genome coverage for all ChIP samples.