GSM3615658: KDM2B_CXXCfl_UNT_gDNA_rep3; Mus musculus; ATAC-seq
Chromatin accessibility was assayed using an adaptation of the assay for transposase accessible-chromatin (ATAC)-seq (Buenrostro et al. 2013) as previously described (King and Klose 2017), using 5x10^5 nuclei. Genomic DNA was also purified from an aliquot of the same preparation of nuclei by phenol-chloroform extraction and tagmented with Tn5, to control for sequence bias of the Tn5 transposase and to determine the exact mouse/fly cell mixing ratio for each individual sample. ATAC-seq and input gDNA libraries were prepared by PCR amplification using custom-made Illumina barcodes (Buenrostro et al. 2013) and the NEBNext High-Fidelity 2X PCR Master Mix (NEB). Libraries were purified with two rounds of Agencourt AMPure XP bead cleanup (Agencourt, 1.5X bead:sample ratio), and were sequenced using the Illumina NextSeq 500 platform in biological triplicate or quadruplicate using 80 bp paired-end reads.