How to start with single-cell transcriptomics
How to start with single-cell transcriptomics
31 October 2025, 9h00-17h00
General context
Single-cell transcriptomics is transforming the way you study cellular diversity and function, making it an essential tool in genomics, molecular biology, and biomedical research. If you are new to the field and want to build a strong foundation before starting your own experiments, this course is for you.
You will learn the key concepts, explore the technologies that power single-cell studies, and discover the latest developments in the field.
- Describe the principles and applications of major single-cell transcriptomics platforms (e.g., 10X Genomics, BD Rhapsody, plate-based systems).
- Differentiate between sample preparation methods for fresh, frozen, and fixed tissues, including single-nuclei sequencing approaches.
- Apply basic criteria to design a single-cell transcriptomics experiment, considering platform choice, sample type, and research question.
- Explain the steps involved in library preparation and sequencing workflows used in core facilities.
- Interpret example datasets to identify key quality control metrics and common data artifacts in single-cell transcriptomics.
- Evaluate the advantages and limitations of emerging technologies such as long-read single-cell sequencing.
- This beginner-friendly course introduces the fundamentals of single-cell transcriptomics, guiding participants through key technologies, experimental design, sample preparation, and basic data quality interpretation to confidently start their own projects.
No prior experience or technical background is required.
The course focuses solely on the practical aspects of setting up single-cell experiments. Participants seeking to learn about data analysis are encouraged to attend our dedicated analysis course: Analysis of single cell RNASeq data.
Trainers
Robin Boiy
Robin Boiy leads the VIB Tech Satellite Antwerp, a hub facilitating access to cutting-edge single-cell technologies within the framework of VIB Single Cell Core and VIB Flow Core. During his PhD, he studied the function of extracellular vesicles in breast cancer, gaining expertise in functional biology and flow cytometry. At VIB Antwerp, Robin provides on-site support for single-cell RNA, ATAC, and multiome workflows, as well as high-parameter flow cytometry and FACS.
Jordy De Coninck
Jordy De Coninck is a bioinformatician at the VIB Single Cell Core, where he develops and maintains data analysis pipelines to support cutting-edge single-cell research. His work focuses on optimizing data management, data processing and ensuring efficient, high-quality data delivery to researchers. With a strong focus on scalability and automation, he helps streamline the flow from raw sequencing data to meaningful biological insights.
Thomas Eekhout
Thomas Eekhout started his PhD in 2013 on plant cell cycle regulation in the group of prof. Lieven De Veylder. After obtaining his PhD in 2018 he did a short postdoc in the same group, after which he joined the plant single cell platform of prof. Bert De Rybel in the summer of 2020. Since then, he has loaded and analyzed over two hundred samples from over 20 species for both internal and external groups on different single cell technology platforms.
Kobe Lavaerts
Bioinformatician at VIB Nucleomics Core in Leuven. Currently mainly focusing on operating and developing routine pipelines for processing raw sequencing data.
Ria Roelandt
Ria Roelandt has a background in molecular biology and bioinformatics. She is single cell expert at the Single Cell Core at VIB. She is responsible for implementing cutting-edge single-cell technologies, scaling new service workflows, developing and teaching single nuclei isolation methods for single nuclei, ATAC or multiome assays.
Jana Roels
Jana Roels is a bioinformatician at the VIB Single Cell Core, focusing on data management and analysis for single-cell genomics. She ensures researchers have streamlined access to datasets and supports their work with computational insights.
Isabelle Scheyltjens
Isabelle did a PhD in the KULeuven lab of Neuroplasticity and Neuroproteomics. To learn more about single cell technologies, she started a Postdoc in the VIB-VUB lab of Myeloid Cell Immunology where she performed the wetlab and analysis of scRNA-Seq on mouse models for Alzheimers Disease, in collaboration with Janssen Pharmaceutica.
Since May 2022, she started a new position in the VIB-KULeuven Center for Cancer Biology (CCB) to dive deeper into the spatial dimension. She became part of the new Single Cell & Spatial Multiomics expertise center to develop, optimize and implement novel spatial and high-plex -omics technologies.
Niels Vandamme
Niels Vandamme heads the VIB Single Cell Core to cover complete experimental and computational workflows for single cell multi-omics. During his PhD, he studied heterogeneity and population dynamics in neural crest biology and cancer cell plasticity, using in vitro systems and genetically engineered mouse models at a single cell resolution. During his postdoctoral training, he gained expertise in computational models to analyze high-throughput single-cell data.
Program
Arrival and coffee (provided)
scRNAseq concepts and platforms
Coffee break (provided)
scRNAseq assays and sample types
Bridging single-cell and spatial: sample type compatibility and workflow synergy
Lunch (provided)
Plate-based single-cell assays
Long read sequencing
Introduction to sequencing platforms
Coffee break (provided)
Interpretation of quality control reports
Multiplexing and demultiplexing strategies (cont.)
Practical info
31 October 2025
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
31 October 2025
Leuven - Campus Gasthuisberg
Leuven train station is approximately 4 km from the campus Gasthuisberg. Buses depart very regularly to the Gasthuisberg Campus from Leuven train station.
For tickets and up to date schedules visit website De Lijn or use the De Lijn App.
Exit at the very last bus stop ‘Gasthuisberg Campus) make sure not to exit at ‘Gasthuisberg Kliniek =
hospital)
Once you get off the bus, go to your right and go up the street until you see stairs to your left. Climb the stairs all the way up between two buildings. Look for the signs containing blue circles and white numbers and follow them all the way from 2 up to number 12. You will cross several buildings and the walk will take max. 10 minutes. When you reach number 12, you have reached O&N 5, where you can find the reception.
31 October 2025
Leuven - Campus Gasthuisberg
The Gasthuisberg campus is west of the Leuven ring. Our buildings are situated behind the hospital (see black arrow near ‘RING NOORD’ on the map). If you come from the city center, you will arrive on campus from the east side (taking Mgr. Van Waeyenberglaan and roundabout Het Teken). If you come from Heverlee or Campus Arenberg, you will arrive from the west side (taking the Celestijnenlaan and Taborweg). When you arrive uphill at the intersection with the Rega Institute and the Red Cross building, you need to take the road down to the bicycle parking at Rega Institute (see map) where you can park. Next, follow the ‘Onderwijs & Navorsing blue route’ description below (start point is #9).
31 October 2025
Leuven - Campus Gasthuisberg
You arrive via the E314 highway – EXIT 16
After 200 m, keep left to drive underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
You arrive via the Leuven ring road
At the roundabout, take the exit towards ‘Spoed / Ziekenhuis’.
Follow the ring around Campus Gasthuisberg and pass the entrance of SPOED.
Continue right until you arrive at a second roundabout.
Follow the directions for E314.
Near the Fire Brigade Station, make a U-turn and follow the directions for ‘Ziekenhuis’.
Keep left and drive downhill, underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
Next, leave the parking at level +1 using the big stairs near the vending machines.
Follow the red carpet and arrows to 'Onco Dagcentrum' to get to the O&N buildings. Take the stairs on your left after exiting Parking West. You are now in front of the O&N4 building; on the left you will find O&N5.