RNA-sequencing of Pyramidal and PV Neurons

Generation of microarray data from pyramidal and PV neurons was previously described [25 (link),26 (link)]. For RNAseq, RNA was isolated using RNeasy micro kits (Qiagen), and cDNA libraries were prepared using the pico input SMARTer stranded total RNA-seq kit (Clontech). Library size was measured by high sensitivity DNA kit (Agilent), and concentration was quantified by Qubit (Life Technologies). Libraries were sequenced on a NextSeq500 (Illumina), and reads were aligned to the human genome using SALMON [27 (link)], and differential expression of genes between cell types was quantified using DESEQ2. On average, 5 million reads mapped to annotated gene regions for each sample. The number of genes with TPM (transcripts per million) >1 was 12,000–13,000 for the isolated cell types, and over 16,000 for slide controls. All data have been deposited to GEO (GSE149154).