High-throughput, single-cell RNA sequencing recently emerged as a powerful tool to profile complex and heterogeneous populations as well as individual isolated cells. This workshop will address the single-cell sequencing workflow from cell preparation (including sorting, sample multiplexing, and cell staining) through cell capture, library preparation, sequencing, and data processing and visualization. Strategies will be defined for enhanced cell enrichment, thereby increasing the purity of the isolated cell and decreasing the costs of sequencing. Additionally, we utilized BD AbSeq™, a novel protein sequencing approach enabled by oligo-conjugated antibodies, for simultaneous detection of mRNA and protein in single cells. A cell-surface antibody panel was created and used for protein profiling alongside gene expression profiling. The antibody-specific oligos were captured, amplified and sequenced alongside mRNAs in a single workflow on the BD Rhapsody™ single-cell analysis system. This workshop will demonstrate a series of standardized experiments that align both flow cytometry and genomic cytometry using a normal mouse model. The addition of protein expression provided more robust clustering of single-cell data compared to clustering by gene expression alone. Comparison of mRNA and protein expression revealed distinct expression profiles for many genes and underscores the importance of multi-omic analysis in single cells. Our study demonstrates the power of combining the BD AbSeq technology with RNA-seq to gain a more comprehensive understanding of cell lineage and function at the single-cell level.