Fig. 1

Isolation of nuclei from frozen brain samples and analysis of ATAC-seq data. Human postmortem frontal cortex was dissociated, nuclei were isolated and stained with the nuclear stain DAPI and a monoclonal NeuN antibody conjugated to PE. a Nuclei were first sorted based on their forward and side scatter from all possible events (R1 gate). b Single nuclei were further sorted based on their size from the doublets or larger clumps of nuclei (R2 gate). c DAPI positive single cells were gated as either NeuN-PE positive (neurons, R3 gate) or NeuN-PE negative (glia, R4 gate). d Post-sort data showing the purity of the separation between neuronal and non-neuronal nuclei. e Fluorescence image showing unsorted nuclei stained for NeuN (red) and DAPI (blue). The scale bar represents 100um. f Proportion of neuronal nuclei from each sample. Error bars show standard error of the mean. g Overview schematic of Levels 1, 2, 3, and 3b of differential analysis. Level 1 compares neuronal vs. non-neuronal for 21 normal and 19 LOAD samples. Level 2 compares normal vs. LOAD for each neuronal and non-neuronal subpopulation. Level 3 compares LOAD samples separated by female and male. Level 3b is the same comparison done after adding 9 female non-neuronal samples (3 normal and 6 LOAD)