RNA-Seq reference-guided workflow with analysis in ArrayStar

RNA-Seq uses next-gen sequencing to show the presence and quantity of RNA in a genome at a particular moment. DNASTAR’s SeqMan NGen application is the starting point for both reference-guided and de novo RNA-Seq workflows. Because this tutorial involves a reference-guided workflow, you will then use ArrayStar to analyze the completed RNA-Seq assembly.

In this tutorial, you will compare stationary phase RNA from wild-type E. coli cells with that from two different mutant cells, each lacking one of two genes that together encode a transcription factor for flagella and chemotaxis operons. An “operon” is a group of one or more genes that are transcribed as a single RNA unit.

In Part A, you will use SeqMan NGen to create a reference-guided DESeq2-normalized RNA-Seq assembly for two experimental replicates and one wild type control of E. coli transcription factors FlhC and FlhD. The data you will assemble is publicly-available single-end Illumina data from E. coli (Fitzgerald et al, 2014). In Parts B & C, you will use ArrayStar to perform downstream analysis and will learn to identify flagella-related operons using two different techniques.

IMPORTANT! There are two options for following this tutorial, one significantly longer than the other.