WIAS course: RNA-seq in Practice: Design to Interpretation

Advances in sequencing technologies and rapidly decreasing costs have made RNA sequencing (RNA-seq) a widely used approach for studying gene expression across a broad range of organisms. Compared with traditional methods such as RT-qPCR, RNA-seq offers higher throughput, greater sensitivity, and the ability to explore transcriptomes at genome-wide scale. As a result, it has become a standard tool in molecular biology, ecology, and genomics research.

This course is intended for PhD students and researchers who have just started to work with, or plan to work with, transcriptomic data. It provides a brief introduction to experimental design, laboratory and library preparation considerations, and their implications for downstream bioinformatic analysis. Participants will gain hands-on experience with established bulk RNA-seq analysis pipelines and learn to critically interpret results from eukaryotic species, including terrestrial and aquatic livestock species. By combining conceptual background with practical data analysis, the course aims to strengthen participants’ confidence in designing, analysing, and evaluating RNA-seq experiments. Finally, the current developments from bulk to single cell/nucleus transcriptomics will also be discussed.

Learning outcomes

Course participants will have increased ability to:

• Understand how to design an RNA-seq experiment
• Examine RNA-seq data from datasets of varying quality
• Apply common practices for RNA-seq analysis, including differential expression analysis
• Evaluate and interpret results from quality control steps, mapping and downstream enrichment analyses
• Assess the advantages and limitations of short-read versus long-read sequencing data
• Understand the principle of single cell/nucleus RNA-seq and its increased value and limitations. 

General information

Target Group	PhD candidates and others interested in RNA sequencing
Course Level	in-depth, post-MSc
Group size	A minimum of 15 and a maximum of 30 participants
Course duration	2 days
Prior knowledge	Knowledge of molecular biology, no previous bioinformatic or unix experience is needed but will be helpful
Homework/ self- study	Literature papers will be provided in advance, and acquaintance of the contents of these papers are expected
Language	English
Credit points	0.6 ECTS
Course content coordinator	Marta Godia Perello
Name lecturers	Marta Godia Perello, Ole Madsen
Venue	Wageningen University campus, Wageningen, the Netherlands. Note: The room and building will be communicated to registered and confirmed participants about one week before the start of the course.

Programme

Day 1

Morning: Experimental design, laboratory and library preparation considerations; RNA-seq data quality control

Afternoon: Mapping, quantification and quality control with PCAs and heatmaps

Day 2

Morning: Differential expression analysis, downstream analysis (Gene ontology enrichment, KEGG pathways)

Afternoon: Short-read vs Long-read RNA comparison; Current developments from bulk RNA-seq to single cell/nucleus RNA-seq

Fee* 

1) Reduced fee: PhD candidates of Wageningen University doing a Training and Supervision Plan (TSP)	€290
2) University fee: All other PhD candidates/postdocs and staff of Wageningen University	€580
3) Other researchers	€870

*(includes study and training material, coffee/tea, and lunches)

Cancellation condition

1. You may cancel free of charge up to 1 month before the start of the course.

2. Cancellation fee of 100% will be applied for persons cancelling less than one month prion to the start of the course or not showing up for the course.

3. The organisers have the right to cancel the course no later than one month before the planned course start date in the case that the number of registrations does not reach the minimum.

More information

Contact: wias@wur.nl. Please note that all email correspondence will go to the email address you provided in the registration.