Identification and functional study of chromatin accessibility in chicken duodenum

The duodenal samples collected in this study were derived from an advanced intercross line (AIL) based on the Lingnan Yellow Chicken line A03 (HQLA) and the Chinese local breed Huiyang beard chicken (HB). Six duodenal samples were collected from 7-week-old chicken. Each sample was then quickly frozen in liquid nitrogen and stored at –80 °C until nuclear extraction was performed. Native nuclei were purified from duodenum samples as previously described. The Nextera DNA Library Preparation Kit (Illumina) was used to perform transposition following the manufacturer’s instructions. In total, 50,000 nuclei were pelleted and resuspended in transposase for 30 min at 37 °C. The transposed DNA fragments were immediately purified using a MinElute PCR Purification Kit (Qiagen). Samples were PCR-amplified using 1× NEBNext High-Fidelity PCR Master Mix (New England Biolabs). Subsequent libraries were purified using MinElute PCR Purification Kit (Qiagen) and sequenced on the Illumina NovaSeq 6000 platform using the PE150 model.