Introduction

This week, we will be exploring how transcriptomics, specifically RNA-seq can be used to study developmental plasticity in non-model organisms. Our research group studies how the phenotype and development of amphibian tadpoles is influenced by different environmental factors, including predator presence, changes in hydroperiod and background colour.

In this course we will discussing how -omics have helped us to answer questions related to this subject. We will also be working through a hands-on example of how we go about evaluating data obtained from an RNAseq experiment.

The practical sessions of this course will heavily rely on the tidyverse in R. This is a great tool that will make working with -omics data much easier. There are many resources online to help you get started, such as this R book by Brendan Ansell.

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Course lecturers

Ivan Gomez-Mestre	igmestre@ebd.csic.es
Christoph Liedtke	christoph.liedtke@ebd.csic.es

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Course Curriculum

Day 1

• Lecture: Introduction to Eco-Evo-Devo. [55 mins]
• Group Discussion: Using transcriptomics to study developmental in non-model systems. [55 mins]
• Practical Preparation: i- A brief introduction to the Tidyverse [Rmd] [20 mins - in your own time]

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Day 2

• Lecture: Pigmentation plasticity in Pelobates tadpoles [PDF]. [15 mins]
• Practical: 01- Exploring RNAseq Counts [Rmd] [answers] [90 mins]

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Day 3

• Practical: 02 - Differential Gene Expression [Rmd] [answers] [50 mins]
• Practical: 03 - DEG visualisation [Rmd] [answers] [30 mins]

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Day 4

• Practical: 04 - Functional Enrichment [Rmd] [answers] [50 mins]
• Group Discussion: Mini exercise, wrapping up and discussing any open questions. [50 mins]

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