GSM1960848: Capan1 5C Rep2; Homo sapiens; OTHER
3C was performed with HindIII restriction enzyme as previously described. For Caco2, Calu3, Capan1, GM12878 and HepG2 cells with two biological replicates for each cell line.  The 3C libraries were then interrogated by 5C.  The region was analyzed by pooling all probes for a final concentration of 0.5 fmol μl−1.  In total, 75 reverse probes and 605 forward probes were pooled for a possible 44,770 interactions.  We included control probes in other regions as follows: Enm002 (Chr5) – 45 reverse probes, Enm004 (Chr22) – 46 reverse probes, Enm008 (Chr16) – 28 probes, Enr311 (Chr14) – 67 reverse probes, Enr112 (Chr13) – 53 reverse probes, Enr113 (Chr4) – 53 forward probes, Enr131 (Chr2) – 65 forward probes, Enr232 (Chr9) – 50 forward probes, Enr233 (Chr15) – 52 forward probes, Enr332 (Chr11) – 42 forward probes.  All probes in these ENCODE regions are the same as previously published.  5C was performed as described with the following changes: 10 ligation reactions were performed for each 5C library, each containing an amount of 3C template that represents 400,000 genome equivalents and 2 fmol of each primer.
GEO Accession
GSM1960848