library_construction_protocol: Confluent cells were recovered by treatment with 0.25% trypsin-EDTA (25200072; Gibco) for 5 minutes at room temperature. Trypsin was quenched with an equal volume of culture medium, and cells were dislodged by flushing the flask surface and collected. The suspension was centrifuged at 800 g for 4 minutes, and the medium was aspirated. Cells were washed once with PBS (pH 7.4; 10010031; Gibco), centrifuged at 800 g for 4 minutes, and the PBS was aspirated. Cells were crosslinked for 10 minutes at room temperature using 10 mL freshly prepared 1% glutaraldehyde (G5882, Sigma-Aldrich) per 10 million cells. The crosslinking reaction was quenched with 10% (v/v) 1.25 M glycine (G7126; Sigma-Aldrich) for 5 minutes at room temperature. Crosslinked cells were pelleted by centrifugation at 2,000 g for 5 minutes, and the supernatant was removed. The pellet was washed with chilled PBS and centrifuged at 2,000 g for 5 minutes. PBS was removed, and cells were washed again with 1 mL chilled PBS per 20 million cells. The suspension was centrifuged at 2,000 g for 3 minutes at 4 °C. PBS was removed, and cell pellets were stored at –80 °C. Tissue was placed in 3 mL ice-cold nuclei extraction buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM Tris-HCl, and 0.1% Triton X-100), freshly supplemented with 30 μL protease inhibitor cocktail (PIC; P8340; Sigma-Aldrich), 3 μL 100 mM PMSF (P7626; Sigma-Aldrich), 3 μL 1 M DTT(43816; Sigma-Aldrich), and 4.5 μL recombinant RNase inhibitor (RRI; 2313B; Takara Bio). The tissue was homogenized on ice using a Dounce homogenizer (D9063; Sigma-Aldrich), with 15 strokes using loose pestle A followed by 25 strokes with tight pestle B. The homogenate was then filtered through a 40 μm cell strainer (22-363-547; Fisherbrand) and centrifuged at 1,000 g for 10 minutes at 4 °C. The supernatant was removed, and the pellet was resuspended in 500 μL nuclei extraction buffer and 750 μL of 50% iodixanol solution (50% iodixanol, 25 mM KCl, 5 mM MgCl2, and 20 mM Tris-HCl [pH 7.8]). Samples were centrifuged at 10,000 g for 20 minutes at 4 °C, and the supernatant was aspirated. The pellets were incubated with 300 μL of 2% normal goat serum (50062Z; Thermo Fisher Scientific) in DPBS (14190144; Gibco), freshly supplemented with 3 μL PIC, 0.3 μL 100 mM PMSF, 0.3 μL 1 M DTT, and 0.3 μL RRI for 10 minutes on ice. Nuclei were resuspended and incubated with 10 μL of 2ng/μL anti-NeuN antibody conjugated to Alexa Fluor 488 (MAB377X; Sigma-Aldrich) in DPBS (1 μg/mL antibody + 499 μL DPBS) on an end-to-end rotator at 4 °C for 1 hour, followed by FACS sorting.  Following FACS, 800 μL PBS, 200 μL 1.8M Sucrose (S0389; Sigma-Aldrich), 10 μL 1M CaCl2 (21097; Sigma-Aldrich), and 3 μL 1M Mg(Ac)2 (M5661; Sigma-Aldrich) were added to each 200 μL of nuclei suspension. Samples were incubated on ice for 15 minutes. Samples were centrifuged at 1,800 g for 15 minutes at 4 °C, and the supernatant was aspirated.  Pellets were resuspended in 9.6 mL PBS per 10 million nuclei. Then, 0.4 mL of 25% glutaraldehyde was added per 10 million nuclei, and samples were crosslinked at room temperature on an end-to-end rotator for 10 minutes. The reaction was quenched with 10% (v/v) 1.25 M glycine for 5 minutes at room temperature. Crosslinked nuclei were pelleted by centrifugation at 2,000 g for 5 minutes, washed with chilled PBS, and centrifuged again. Nuclei were washed once more with 1 mL chilled PBS per 20 million nuclei and centrifuged at 2,000 g for 3 minutes at 4 °C. Nuclei pellets were stored at –80 °C. Libraries from human PFC, mouse cortex and Gomafu in HeLa cells were prepared using the Takara DNA Thruplex Kit, while remaining cell line libraries were prepared with the IDT ACCEL-NGS 2S DNA Library Kit, following manufacturer protocols. Library amplification was performed by real-time qPCR (1855200; Bio-Rad) following the corresponding PCR protocol for each kit. Amplification was stopped once fluorescence increased by 1,500 RFU above baseline. Samples were purified using SPRI magnetic beads (B23317; Beckman Coulter) and the fragment size was measured using the Agilent TapeStation. The KAPA Library Quantification Kit (Roche Diagnostics) was used according to the manufacturer's protocol to measure library concentration. Libraries were pooled such that approximately 50 million raw reads were allocated to each sample and sequenced on a NovaSeq X instrument to generate 150-bp paired-end reads.