To build an atlas of cell populations and cell-type-specific gene expression patterns across the adult (P60–70) mouse brain, we prepared single-cell suspensions (STAR Methods) from nine brain regions (Table S1 and Data S1) and used Drop-seq (Macosko et al., 2015) to profile the RNA expression of 690,207 individual cells (Figure 1A). The resulting cell suspensions, which recovered intact 40–50% of cells from most tissues (cortex: 0.46 ± 19 mean ± sem; striatum: 0.39 ± 20, Figure S4A–C), had cells with morphologies characteristic of neurons, astrocytes, and oligodendrocytes (Figure S1A). We generated and analyzed 13 billion sequencing reads from the resulting Drop-seq libraries, detecting 1.45 billion distinct mRNA transcripts (UMIs), which arose from 31,767 distinct genes. We ascertained an average of 17,480 reads (median=10,824), 2,218 mRNA transcripts (median=1,450 UMIs), and 1,169 genes per cell (median=900).
