title: ATAC-seq of Zonotrichia albicollis: adult male hypothalamus (white morph)
design: 10,000 - 200,000 cells were homogenized in EMEM (Eagles Minimum Essential Medium) and phosphate-buffered saline. The cells were pelleted in a centrifuge and re-suspended in a lysis buffer made of non-ionic detergent (made in-house from Tris, NaCl, MgCl2, and IGEPAL CA-630).  After cell lysis, nuclei were isolated by centrifugation and added to a tagmentation reaction mix (Illumina Nextera DNA Library Prep Kit, Cat#: FC-121-1030). During tagmentation, the sequencing adapters were inserted into accessible chromatin regions by Tn5 transposase. Adapter-tagmented fragments were purified (Invitrogen Agencourt AMPure XP beads, Cat#: A63880), bar-coded (Illumina Nextera Index Kit, cat#: FC-121-1011), and amplified (Fisher KAPA HiFi HotStart Kit, Cat#: NC0295239). The ATAC-seq libraries were then sequenced using a MiSeq sequencer (Illumina; Reagent Kit v3) with 150 cycles (75 bp paired-end reads) in the Molecular Evolution Core at Georgia Tech.