title: GSM3133247: 5C-insitu-mEs-2i-GenomeCopies-5k; Mus musculus; OTHER
library_construction_protocol: 3C templates were generated using HindIII with a in situ 3C protocol similar to that previously described in Rao et al. 2014. 5C libraries were generated from 5,000 genome copies of 3C templates using double alternating 5C primer design across ~1-3.5 Mb regions around Sox2, Klf4, Dppa2, Rex1, Nanog  (described previously Dostie and Dekker, 2007; Dostie et al., 2006; van Berkum and Dekker, 2009; Hnisz et al 2016). Library was constructed using NEBNExt Ultra DNA Library prep kit for Illumina kit according to manufacturer's protocol. Each library was quantitated using qPCR-based Kapa Library Quantification Kit, and equal molecular number of each libarary was pooled before sequencing.