Following single-cell dissociation or nuclei isolation, the Next GEM 3' assay uses microfluidics to partition and assign cell- or nuclei-specific barcodes to transcript cDNA at the 3' end. Barcoded cDNA is prepared with adaptors for sequencing by synthesis (SBS). The following protocol has been adapted from protocols developed by 10x Genomics 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.