Figure 2.

Use of nanodroplets does not influence detection of chromatin accessibility. (A) Normalized sequencing tracks of FAIRE-seq signal without (lavender) or with (dark purple) nanodroplets (EWS894). Signal for each replicate is shown. Regions of enrichment shared across all replicates are highlighted in blue. (B) Top two principal components of mean FAIRE-seq signal in 300-bp windows genome-wide across EWS894 (purple) and HUVEC cell lines (blue) identified by FAIRE with and without nanodroplets. Each symbol represents a FAIRE-seq replicate data set. Circles denote signal identified by FAIRE without nanodroplets, inverted triangles by nanodroplet FAIRE. (C) Spearman's correlation heatmap of genome-wide FAIRE-seq signal (300-bp windows) across replicates in EWS894 and HUVEC cell lines (lavender and sky blue, without nanodroplets; dark purple and blue, with nanodroplets). Clustering distances across samples determined by the nearest point algorithm depicted by tree on the left. (D) Normalized mean EWS894 FAIRE signal by FAIRE without nanodroplets (lavender) and with nanodroplets (dark purple) at all transcription start sites with non-zero signal genome-wide. Signal ±1.5 kb around transcription start sites is shown. (E) Signal around regions of enrichment for each replicate of EWS894 FAIRE signal found by FAIRE with and without nanodroplets. Signal enrichment ±2 kb around peak center shown. All heatmaps sorted by sum of signal in each peak set within which peaks were called. (F) Bar plot of the percentage of peaks at genomic locations called from EWS894 and HUVEC FAIRE in each replicate found without (lavender and sky blue, respectively) and with nanodroplet FAIRE (dark purple and blue, respectively). (G) Enriched motifs identified at union set of peaks identified from pooled replicates of EWS894 FAIRE signal found by FAIRE with and without nanodroplets. Motifs are plotted base on rank (x-axis) and enrichment P-value (y-axis). ETS-containing motifs are shown in purple.