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In this tutorial you will learn to compare expression levels using RNA-seq data from 2 sample conditions, where each sample has 3 replicates.
The basic Geneious Expression Analysis tutorial covered the use of Geneious's built-in RNAseq expression analysis tools. This tutorial uses Geneious's implementation of the R package DESeq2, which should be used when you have multiple replicates for each sample condition.
This tutorial uses a sample dataset from Vibrio fischeri, a marine bioluminescent bacterium which is the monospecific symbiont of the Hawaiian bobtail squid, Euprymna scolopes. These bacteria colonize the light-emitting organ of E. scolopes, providing a light source for the squid's nocturnal antipredatory behavior.
The RNAseq datasets are from a study by Luke Thompson et al, investigating transcriptional changes that the bacteria undergo in the early stages of colonizing the squid host. RNAseq experiments were performed on V. fischeri cells in culture, cells that were incubated in artificial seawater, and cells collected during expulsion from the squid host in order to look for changes in gene expression that were directly associated with host colonization.
The full datasets from this study can be downloaded from NCBI, under BioProject PRJNA319479.
Exercise 1: Data preparation and mapping
Exercise 2: Calculating expression levels.
Exercise 3: Comparing expression levels with DESeq2
If you want to open the tutorial in a different window, click the new window button .