Combinatorial barcoding is an instrument-free method used to generate single-cell and single-nucleus RNA-sequencing libraries. Outlined here are the methods used to isolate single-nuclei from frozen tissue; to fix nuclei following isolation; to ligate nuclei-specific barcodes to transcript cDNA by iteratively splitting and pooling nuclei suspensions between multiple 96-well plates via the Evercode WT system; and to prepare barcoded cDNA for sequencing by synthesis (SBS). The following protocol has been adapted from protocols developed by 10x Genomics, Parse Biosciences, and Illumina to be used at the University of Minnesota TMCs in collaboration with the University of Minnesota Genomics Center. These protocols are owned by their respective companies and are subject to periodic revision.