Extended Data Fig. 8: Experimental design for RNAseq analysis of single nuclei isolated from cortex and hippocampus of wild type and 5xFAD mice with and without ACE expression in microglia.

a, Single nuclei were isolated from cortex and hippocampus of 9-month-old mice, and pooled into samples representing two mice from each genotype and sex (SN1-8). The samples were divided into two groups (Group 1 and Group 2) containing 4 samples that were each labeled with a unique hash-tag antibody. b, The samples were sorted using fluorescence activated nuclear sorting to capture nuclei in the P1 gate that were enriched for microglia by rejecting many neurons (NeuN+), oligodendroglia cells (Sox10+) and astrocytes (Sox9+). c, cDNA libraries were generated from Group 1 and Group 2 samples and the sequences were demultiplexed into samples according to the antibody hash-tag that was used to label the nuclear samples (SN1-SN8). Nuclei that were labeled by more than a single hash-tag antibody (cell colored red) were removed from the datasets within each sample. The TotalSeq hash-tag antibody used and the number of single labeled nuclei per sample are shown.