GSM6042848: HPC5_ATAC; Mus musculus; ATAC-seq
100,000 Nfix+/+ HPC5 cells were lysed and nuclei were resuspended using the Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (20034197, Illumina; San Diego, CA). Following purification with Zymo DNA Clean and Concentrator-5 kit (D4014, Zymo; Irvine, CA), libraries were amplified using NEBnext PCR master mix (M0541S, New England BioLabs; Ipswich, MA) and custom Nextera PCR primers for five cycles (custom primers from Buenrostro et al.70) . The degree of library amplification to reduce GC and size bias was determined using quantitative PCR using SYBR Gold reagents (S11494, Invitrogen; Waltham, MA). A total of 9-10 cycles were performed and libraries were purified using a Zymo DNA Clean and Concentrator-5 kit (D4014, Zymo; Irvine, CA) or Qiagen MinElute Kit (28004, Qiagen; Hilden, Germany). Eluted libraries were further purified using the E-Gel system (Invitrogen; Waltham, MA). An E-Gel 2% agarose gel (G402002, Thermo Fisher; Waltham, MA) was run and fragments between 100bp and 1000bp were excised followed by clean up with Zymo Clean Gel DNA (D4008, Zymo; Irvine, CA). Purified libraries were submitted to the Hartwell Center for Biotechnology for sequencing.