RNA sequencing (RNA-Seq) is a widely used experimental approach in molecular biology. RNA-Seq allows us to measure the level of RNA in cells and tissues, and therefore make inferences about what genes are active, under what circumstances, and when. Analysis of an RNA-Seq experiment typically uses tools which are designed for the Linux command line. While these tools can be intimidating, Jupyter Notebooks (https://jupyter.org/) are a popular data science platform that makes command line easier to use. In this series, we will examine an RNA-Seq dataset using Jupyter and learn how to use important bioinformatics tools including the NBCI Sequence Read Archive (SRA), Kallisto, and the UCSC genome browser.