Single-nucleus RNA-seq in the post-mortem brain in major depressive disorder

We performed high-throughput snRNA-seq using the 10X Genomics Chromium platform on archived post-mortem dorsolateral prefrontal cortex (BA9) tissue in MDD subjects who died by suicide and in control subjects to identify cell-type specific differentially expressed genes. Overall design: 10X Genomics Chromium snRNA-seq was performed on nuclei extracted from BA9 of the post-mortem brain tissue of 17 control subjects and 17 MDD cases who died by suicide. All subjects were male. Cell-types were identified by unsupervised clustering and diffrential gene expression was performed between cases and controls for each cell-type cluster. The library preparation was performed with the Chromium Singel Cell 3' Reagent Kits v2. Paired-end sequencing was performed on the HiSeq Illumina 4000. FastQ files were produced with Cellranger v2.1.0 mkfastq. Alignments and gene counts were generated with Cellranger v2.1.0 count.