This 5-day course aims to provide an entry point to understand the principles of RNA-sequencing (RNA-seq) data analysis, covering both bulk and single-cell RNA-seq (scRNA-seq). Students will learn the practicalities of RNA and scRNA sample preparation, data generation, data cleaning, processing, analysis and interpretation. By directly comparing both methods, students will also develop a critical understanding of the most appropriate application for each technology.
Registration is closed, since the course has reached the maximum number of participants.
Course coordinator
Dr. Miaomiao Zhou, Avans University of Applied Sciences
Co-organisers
Dr. Miaomiao Zhou1, Dr. Nikolaos Strepis2 and Dr. Willem de Koning3
- Centre of Expertise Material and Energy Transition, Avans University of Applied Sciences
- Department of Pathology and Clinical Bioinformatics, Erasmus MC
- Department of Pulmonary Medicine, Erasmus MC
Course credits
1.5 ECTS for following the course.
Location
Avans University of Applied Sciences
Hogeschoollaan 1
Room HA209
4818CR Breda, the Netherlands
Course description
This intensive 5-day course provides training across the full spectrum of RNA-sequencing data analysis. It is organized by the BioSB research school in collaboration with Avans University of Applied Sciences and Erasmus MC.
The programme bridges the gap between traditional bulk analysis and high-resolution single-cell techniques. Participants will start with the fundamentals of experimental design and preprocessing before diving into analysis pipelines for bulk RNA-seq (including differential expression and variant calling) and scRNA-seq (including clustering, trajectory inference, and batch correction).
The course features a dynamic mix of expert lectures and extensive hands-on practicals, primarily using R, with supporting modules in Galaxy and Linux. We will also explore the potential of long-read sequencing, spatial transcriptomics, and the use of AI to enrich data analysis and interpretation. The course concludes with a journal club session designed to improve skills in reading, understanding and drafting scientific manuscripts that use RNA-seq data.
Learning objectives
Upon completion of this course, participants will:
- Understand the principles of bulk RNA-seq and scRNA-seq experimental design
- Be able to preprocess and analyse bulk RNA-seq and scRNA-seq data, from quality control to downstream analysis
- Gain expertise in the application of bulk RNA-seq and scRNA-seq for clinical and research purposes
- Learn to apply statistical methods for identifying differentially expressed genes and variants in both bulk and single-cell data
- Be able to perform clustering, classification, and pathway analysis on bulk RNA-seq and scRNA-seq data
- Understand how artificial intelligence (AI) can enhance RNA-seq data analysis and inform academic research
Target audience
This course is aimed at researchers and professionals with experience in next-generation sequencing (NGS). The content is designed to provide both a deep understanding of bulk RNA-seq and scRNA-seq data analysis, including pipeline design, computational tools, and cutting-edge techniques for data analysis. While prior experience with programming is beneficial, minimal programming experience is expected. The course is suitable for participants who are comfortable with the basics of bioinformatics tools and software, but may not be experts in coding.
Lecturers
Bulk RNA-seq
Andrew Stubbs, Bazante Sanders, Georgios Gavriilidis. Martina Summer-Kutmon. Miaomiao Zhou, Nikolaos Strepis, Victoria Aguilar Pontes, Willem de Koning, Tim Verschuren
Single-cell RNA-seq
Andrew Stubbs, George Karakatsoulis, Georgios Gavriilidis, Martina Summer-Kutmon, Nikolaos Strepis, Willem de Koning
Detailed course program
Daily schedule of the course.
Additional information
For more information about the course, please contact the BioSB community manager.
Wildcards
If you would like to join this course using a wildcard, please contact the BioSB community manager.
Until the maximum number of wildcard spots is reached, you can register with a wildcard until 20 April 2026. Always mention in your application from which academic group the wildcard comes. Your registration is only valid after confirmation.
Registration
- € 480 (excl. VAT) for PhD/MSc students
- € 720 (excl. VAT) for academic researchers (non-profit)
- € 1080 (excl. VAT) industry participants (for profit)
Course fees includes course materials and catering (coffee, tea and lunch).
Registration is closed, since the course has reached the maximum number of participants.
Find general enrollment information here.
