title: GSM3504381: YAP5SA CM 4C-seq Nog rep2; Mus musculus; OTHER
library_construction_protocol: Approximately 5 million bead-bound PCM1-enriched cardiomyocyte nuclei, isolated as described above, were used as input for each replicate. The 4C protocol was performed as described previously (van der Werken et al. 2012, Methods in Enzymology), with minor modifications. The first restriction enzyme digestion was performed with DpnII (NEB, R0543M). The first ligation was perfromed overnight with T4 DNA ligase (Roche, 10799009001). Samples were then de-crosslinked with Proteinase K (Thermo Fisher, EO0491) overnight. DNA was purified using P-beads from the NucleoMag 96 PCR kit (Macherey-Nagel, 744100.1). The second enzymatic digestion was performed overnight with Csp6I (Thermo Fisher, ER0211). Samples were then ligated, as described above, overnight and purified with NucleoMag P-beads. We then employed a 2-step PCR protocol to amplify DNA and generate libraries for sequencing. All PCR reactions were carried out with Expand Long template polymerase (Roche, 11681842001). Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, A63881), at 0.8X. Finally, all libraries were sequenced on an Illumina Nextseq 500.
attributes.tag: GEO Accession
attributes.value: GSM3504381