Extended Data Figure 4. Replicate data showing gene activation from a close enhancer is not affected by cohesin depletion.

(a) Percentage of (left axis) Shh and (right axis) Lmbr1 expressing alleles, assayed by RNA FISH, in TALE-transfected SCC1-AID cells either untreated (- auxin) or treated with 6 hours of auxin (+ auxin). Cells were transfected with tSBE6-VP64 or tSBE6-VP64 -Δ. Data shown are from one biological replicate. Data from an independent biological replicate are shown in Fig. 4a. The data were compared using a two-sided Fisher’s Exact Test, n = numer of alleles scored, ns – not significant. Source Data EDFig4. (b) Table showing two-sided Fisher’s Exact Test p-values for differences in the percent of Shh-expressing alleles in TALE-transfected wild type ESCs and SCC1-AID cells assayed by RNA FISH in the absence or presence of auxin. Cells were transfected with SBE6-VP64 and SBE6-Δ. Data from Figure 4a and Extended Data Figure 4a. p-values in bold are significant (<0.05). (c) Table showing the two-sided Mann-Whitney U p-values for differences in the Shh-SBE6 inter-probe distances between the data from SCC1-AID ESCs with or without the addition of auxin and transfected with either tSBE6-Vp64 or tSBE6-Δ. No of alleles scored is indicated (in parentheses). p-values in bold are significant (<0.05). Also shown are the median and interquartile distances of each data set. Data are from Figure 4c.