This repository contains R code for subclustering medium spiny neurons (MSNs) from a rat nucleus accumbens (NAc) single nucleus RNA sequencing data set. Code producing additional plots is also included.
A single-nucleus transcriptomic atlas of medium spiny neurons in the rat nucleus accumbens Benjamin C. Reiner, Samar N. Chehimi, Riley Merkel, Sylvanus Toikumo, Wade H. Berrettini, Henry R. Kranzler, Sandra Sanchez-Roige, Rachel L. Kember, Heath D. Schmidt, Richard C. Crist bioRxiv 2024.05.26.595949; doi: https://doi.org/10.1101/2024.05.26.595949 https://www.biorxiv.org/content/10.1101/2024.05.26.595949v1
snRNA-seq count matrices for our discovery dataset are available at the NCBI Gene Expression Omnibus (GEO) under accession number GSE263307. The raw count matrices used in the replication analysis are available at GEO accession numbers GSE137763 and GSE222418. Cleaned data from mouse and human NAc can be obtained at GEO accession number GSE118020 and https://github.com/LieberInstitute/10xPilot_snRNAseq-human, respectively.