Figure 1

(a and b) Numbers of overlapping FAIRE peaks between control and differentiation-induced cells at 24 and 144 h. (c) Genes for the 24 h control sample were split into quartiles based on reads per kilobase per mapped million (RPKM) in RNA-seq data, high RPKM ≥10, medium RPKM ≥1<10, low RPKM >0<1, zero RPKM=0. (d) FAIRE peaks were labelled based on the high, medium or zero expression of the nearest-neighbour gene. FAIRE peaks were in this case more often near genes with expression above zero. Data representative of all time points. (e) Position of FAIRE peaks relative to annotated genomic features demonstrated that the majority of peaks were intronic or intergenic. The greatest variation between samples was seen within the proportion of peaks at promoters directly upstream of a transcription start site, with increases in the proportion of FAIRE peaks at these sites in both differentiated time points relative to their non-differentiated controls