design: Chromatin accessibility profiling of the pig limbic and endocrine tissues
library_construction_protocol: Animal handling and compassionate euthanasia were performed in compliance with pertinent ethical laws, standards, and regulations. The study included 8 female German Landrace pigs, with an average age of 170 ± 14 days and weight of 105 ± 8 kg. The adrenal gland and brain tissues, including the amygdala, hippocampus, hypothalamus, pituitary gland, and thalamus were dissected and cryopreserved in liquid nitrogen tank until analysis. ATAC-seq libraries were generated using a protocol for cryopreserved nuclei (Buenrostro et al., 2015; Halstead et al., 2020). Essentially, tissues/cells were lysed to release nuclei and density gradient centrifugation with iodexanol was employed to eliminate contaminating mitochondria. Nuclei were counted using Trypan solution to assess the optimal viable nuclei for transposition using Illumina Tagment DNA Enzyme and Buffer Kit (Tn5 Transposase/Tagment DNA Enzyme 1) according to the manufacturer's protocol (Illumina, San Diego, CA, USA). Tween 20 and Digitonin were added to the transposition reaction to increase nuclear permeabilization and efficiency. PCR was performed to amplify transposed fragments and tag individual sample using the Illumina unique dual indexes. The libraries were quality control on DNA chip using Agilent Bioanalyzer 2100.