Nuclei were isolated from snap frozen mouse liver tissues according to a previously published protocol (dx.doi.org/10.17504/protocols.io.bhpej5je), for a total of two replicates for the young and aged conditions. Briefly, samples were prepared by incubating fresh tissue chunks in HypoThermosol FRS solution (Sigma Aldrich, cat. no. H4416) for 15 minutes on ice, followed by a 30-minute incubation in Cryostor CS10 cryopreservation medium (Stemcell Technologies, cat. no. 7930) on ice, subsequently transferred to a cryo-freezing container overnight at -80° C and then to liquid nitrogen storage. Frozen liver tissue was minced into small chunks and homogenized in a refrigerated Dounce homogenizer using lysis buffer prepared according to the protocol's instructions. After thorough homogenization, lysate was transferred into a 15-mL Falcon tube through a 40 mM cell strainer and samples were spun for 5 minutes at 500g at 4° C. Nuclei were counted using a hemocytometer and 10, 000 nuclei per sample were loaded onto the Chromium Single Cell 3′ Chip (10X Genomics, USA) and processed with the Chromium Controller (10X Genomics, USA). Library was performed according to the manufacturer's instructions (single cell 3' v2 protocol, 10X Chromium).