Single-cell RNA-seq of Mouse Cortical Cells

Dissociated cortical cells were resuspended in PBS, filtered through a 70 micron cell strainer followed by a 40 micron tip strainer, and counted with a Countess instrument (Life Technologies). The cells were further diluted to the final concentration (80,000 cells/mL) with OptiPrep (Sigma) and PBS, and the final concentration of OptiPrep was 15% vol/vol. A total of 2,000 to 5,000 cortical cells were collected per mouse and processed following the InDrop protocol [38 (link),110 (link)]. Final libraries containing ~1,200 cells were constructed and sequenced on an Illumina NextSeq 500 instrument, generating on average ~130 million reads per library (S3 Table).