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.


Data and Resources

Raw Files [34]

Additional Info

Field Value
Type of Data

Expression profiling by high throughput sequencing


RNA Sequencing

GSE Submission Date 23/01/2020
GSE Authors Gustavo,,Turecki
Dataset Last Updated December 7, 2020, 11:29 (UTC)
Dataset Created December 7, 2020, 11:28 (UTC)