2025-07-31
ENA first public
ERC000011
ENA-CHECKLIST
Research Institute for Farm Animal Biology (FBN), Physiological Genomics
INSDC center name
public
INSDC status
ERS23784487
SRA accession
E-MTAB-14923:amy_13
Submitter Id
170
day
age
ArrayExpress
broker name
not collected
collection date
pig
common name
Protocols: 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.
description
adult
developmental stage
wild type genotype
genotype
not collected
geographic location (country and/or sea)
not applicable
individual
not applicable
isolate
Sus scrofa
organism
Sus scrofa
organism
amygdala
organism part
Sus scrofa
scientific_name
female
sex
German Landrace
strain
amy_13
title