 Abstract RNA sequencing, INasec, is a genomic approach for detecting and quantifying messenger RNA molecules in biological samples, useful for studying cellular responses. However, SCINasec allows direct assessment of the fundamental unit of biology, the cell, and is now accessible to any biomedical researcher or clinically in with increasing commercial availability of platforms and maturing bioinformatics approaches. This review presents a practical guide for designing SCINasec studies, including experimental hardware, protocol choice, quality control, data analysis, and biological interpretation. This article was authored by Ashraf al-Haq, Jessica Engel, Sarah A. Teachman, and others.