Mice were anesthetized and perfused through the left cardiac ventricle by injecting cold phosphate-buffered saline (PBS). The brain was homogenized using a gentleMACS Dissociator (Miltenyi Biotec) and enzymatically digested with a collagenase/DNase I solution at 37 °C for 45 minutes. Cells were passed through a 70-μm cell strainer into a new tube for Percoll gradient centrifugation. Then, cells were removed from the interphase and washed with PBS. Leukocytes were labeled with an anti CD45–BV480 antibody. The cells were re-suspended in PBS supplemented with 10 % FBS, and viable CD45HIGH cells were sorted on a FACSAria Fusion (Becton Dickinson). Both the 3xTg-AD and wild-type samples consisted of > 98% viable cells.  CD45HIGH cells were resuspended to a final concentration of 700 cells/µl. cDNA sequencing libraries were prepared using the 10´ Genomics Chromium Controller and the Chromium Single Cell 3′ GEM, Library and Gel Bead kit v3 (Pleasanton) following the manufacturer's instructions. Briefly, 10,000 live cells were loaded onto the Chromium Controller to recover 4000 single-cell gel-bead emulsions (GEMs) per inlet, uniquely barcoded. After cDNA synthesis, sequencing libraries were generated and final 10× library quality was assessed using the Fragment Analyzer High Sensitivity NGS kit (Agilent Technologies) before sequencing on the Illumina NextSeq500 platform, generating 75 bp paired-end reads (28 bp read 1, 91 bp read 2) at a depth of 50,000 reads per cell, yielding a median per-library depth of 72,783 reads per cell.
GEO Accession
GSM4697522