This is analysis of integration data on the chromosome to determine if there is any site bias

sample.name CtcfO Elon ElonW Enh EnhF1 EnhF2 EnhPr EnhW Gen5’1 Gen5’2 Low1 Low2 Low3 Low4 PromF PromP1 PromP2 Quies Repr1 Repr2 Repr3 Repr4 Repr5 Repr6 Tss
JS69_-v:ND 0 2 0 0 0 0 2 2 0 2 0 0 2 2 0 0 0 2 2 2 2 2 2 2 0
JS70_-v:RAL 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 0
JS71_v:ND 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS72_v:RTX 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS73_v:RAL 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS74_v:RTX:RAL 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS77_v:ND:UDG 0 2 2 0 2 2 2 2 2 2 2 2 2 2 2 0 2 2 0 2 2 2 2 2 0
JS78_v:RTX:UDG 2 2 2 0 2 2 0 2 2 2 2 2 2 2 0 0 0 2 2 2 2 0 2 2 0
JS79_v:RAL:UDG 0 2 2 0 2 2 0 2 2 2 0 2 2 2 2 2 2 2 0 2 2 2 2 0 2
JS80_v:RTX:RAL:UDG 0 2 2 0 0 2 2 0 0 2 0 2 2 2 0 0 2 2 0 2 2 0 2 2 2
JS81_-v:ND 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 0 0 2 2 2 2 2 2 2 2
JS82_-v:RAL 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS83_v:ND 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS84_v:RTX 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS85_v:RAL 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS86_v:RTX:RAL 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
sample.name CtcfO Elon ElonW Enh EnhF1 EnhF2 EnhPr EnhW Gen5’1 Gen5’2 Low1 Low2 Low3 Low4 PromF PromP1 PromP2 Quies Repr1 Repr2 Repr3 Repr4 Repr5 Repr6 Tss
JS69_-v:ND 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS70_-v:RAL 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS71_v:ND 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS72_v:RTX 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS73_v:RAL 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS74_v:RTX:RAL 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS77_v:ND:UDG 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS78_v:RTX:UDG 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS79_v:RAL:UDG 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS80_v:RTX:RAL:UDG 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS81_-v:ND 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS82_-v:RAL 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS83_v:ND 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS84_v:RTX 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS85_v:RAL 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
JS86_v:RTX:RAL 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

Graph 1 shows the correlations between chimeras and discordant reads in each sample. Samples that should not have integrations have low levels of correlation(flat line), this may be expected if the integrations are noise in the data or false positive results. Graph 2 shows where these integrations occur in relation to hepG2 segmentation analysis. This gives a general indication of bias towards these regions. In the +RTX(graph 3) situtation we see enhancement in open chromatin (genes, enh, prom) and supressed in closed chromatin. Open treatment with RAL the pattern changes(increased in promoters and TSS), this may be due to the lower number of integration events or may be a real pattern (graph 4). Additional repetitions may be necessary to suss this out. These tables show the number of discordant and chimeric reads in each segment.