Psilocybin Cortex snRNAseq

This repository contains analysis scripts for the manuscript "Single-nucleus transcriptomics reveals time-dependent and cell-type-specific effects of psilocybin on gene expression" by Liao et al, 2025.

This study is a collaboration between

• the Alex Kwan lab at Cornell University (Meinig School of Biomedical Engineering)
• the Kenneth Kwan lab at University of Michigan (Michigan Neuroscience Institue, Department of Human Genetics)

Usage

Reads (fastq) processing

Raw fastq files can be downloaded from the SRA Accession. Per cellranger v7.1.0 docs, each sample should be in its own directory entitled with the sample name (ie. 4797-CL-1/) Files split into different sequencing lanes should be concatenated. (Note that the 4 samples requiring concatenation were all excluded from the analysis due to oversequencing). Processing should follow the Methods section of the manuscript. The provided Snakefile can be used as a template but was built specifically for the authors' file system.

Cell-gene matrix processing

Loading the matrices, quality control and preprocessing, transformations, UMAP embeddings, and clustering can be found in the notebooks folder. This also includes differential expression analysis using the memento package.

Figure generation

Code to generate figures appearing in the paper and supplement can be found in the paper_figures folder.

Correspondance

Please refer to manuscript for correspondance details