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4C-seq libraries were generated from S2 cells. Nuclear extraction and crosslinking were carried out as described in Hi-C experimental procedure above. The remainder of the 4C-seq procedure was carried out as previously described [57]. Csp6I, DpnII or NlaIII were used as primary or secondary restriction enzymes. Primer sequences for each viewpoint and condition were generated using 4C primer design (https://mnlab.uchicago.edu/4Cpd/) and are listed in Additional file 4: Table S2. Independent biological replicates of multiplexed libraries were sequenced on separate lanes of an Illumina Hi-Seq 2500 configured for 150-bp paired-end reads.

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