library_construction_protocol: iSCI mice were perfused with ice-cold PBS with heparin at 3, 7 or 28 dpi, spinal cords dissected out and 4 mm of spinal cord rostral (T9-T11) and caudal (L1-L3) to the lesion epicenter were then rapidly removed, snap-frozen in dry ice and stored at -80°C. An anatomically equivalent region of spinal cord (T11-L1) was isolated from age- and genotype-matched healthy controls. Frozen tissue was homogenized in Homogenization buffer (320 mM Sucrose, 0.1mM EDTA, 0.1% IGAPAL, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris, Roche Protector RNAse Inhibitor, Complete Roche Protease Inhibitor Version 12, 0.016mM PMSF, 0.166mM b-Mercaptoethanol; pH=7.8). Nuclei were isolated from the homogenate by iodixanol gradient and resuspended in 1% BSA solution before proceeding immediatly to 10x single cell RNA-sequencing snRNA-Seq libraries were prepared using 10x Chromium Next GEMSingle Cell 3 (v3.1) per manufacturer's instructions. Samples were loaded to capture 10,000 nuclei per sample. During library preparation, the initial cDNA amplification was run for 13 cycles, which was found to be optimal for 10,000 nuclei. Sequencing: 2x150 reads base pairs (bps) , ~40,000 reads/cell