library_construction_protocol: Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation. For RNA extracted from distal stump samples, RNA concentration was determined with a Nanodrop and integrity assessed on a Fragment Analyzer. For RNA extracted from distal stump samples, rRNA was depleted from 100ng total RNA input using the RiboZero Magnetic Gold H/M/R Kit (Illumina). Directional RNA-seq libraries were prepared from rRNA-depleted RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs). For RNA extracted from 1000 FACS-sorted macrophage and Schwann cells, cDNA was generated and amplified with the SMART-Seq v4 Ultra Low Input RNA Kit (Takara);  RNA-seq libraries were prepared with the NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs) using 4ng amplified cDNA from macrophage samples and 1.5ng from Schwann cell samples.