library_construction_protocol: Cultured cell line or isolated nuclei from primary brain cortex were processed with Hi-C 3.0 protocol. Cells were firstly double-crosslinked with PFA followed by DSG, then treated with SDS and Triton X-100 to open chromatin. Then the chromatin was digested by resuspending the nuclei in digestion mix containing DdeI and DpnII without detergent, and incubated at 37°C for 2 hours, followed by inactivating the REs. The DNA ends was filled by biotin labeled dATP, followed by proximity ligation using T4 ligase by incubating at room temperature for 2 hours. For sample prepared for dscHi-C multiome experiment, all reaction mix was supplemented 0.5 U/μL Protector RNase inhibitor. Nuclei processed through Hi-C 3.0 procedure were bulk tagmented with Tn5 transposome, then loaded to 10x Chromium platform according to either ATAC kit or multiome kit. For dscHi-C, the DNA were barcoded by linear amplification in droplet, followed pooling droplets, further amplification and sample index were incorporated. For dscHi-C-multiome, the DNA and RNA from the same cell were barcoded in droplet, the then droplets were pooled and nuclei were decrosslinked. Genomic DNA were pull down using streptavidin beads, and cDNA were further proceeded with second time reverse transcription. Then the genomic DNA were direct subjected to library preparation. The cDNA were further fragmented and amplified for library construction.