 Abstract RNA sequencing, INA-SEC, is a genomic approach for detecting and quantifying messenger RNA molecules in biological samples, useful for studying cellular responses. However, SC-INA-SEC allows direct assessment of the fundamental unit of biology, the cell, and with increasing commercial availability and maturation of bioinformatics approaches. Any biomedical researcher or clinically in can use it to make discoveries. This review presents a practical guide for designing SC-INA-SEC studies, including experimental hardware, protocol choice, quality control, data analysis, and biological interpretation. This article was authored by Asher for Huck, Jessica Engel, Sarah A. Teachman, and others.