Single cell transcriptomics summer school
Single cell transcriptomics summer school
09/09/2024 - 12/09/2024
General context
Registration deadline: 15th of August 2024
The kick-off day on 9 September is open to everyone and free. It features a comprehensive overview of single cell transcriptomics, designed for those looking to understand the basics, get started with single cell omics, and navigate the latest advancements in the field.
In the next three days, we will go through the entire workflow from data acquisition to data analysis. At the end of the course, attendees will better understand the dos and don’ts in single cell transcriptomics and they will be able to set up and analyze their own experiments.
The summer school is organized with the support of 10x Genomics and Element Biosciences.
The kick-off day will feature a mix of technical and general talks, ensuring that everyone will gain valuable insights. We will cover:
- Recent developments in various technology platforms, including 10X Genomics, BD Rhapsody, and Smart-seq, along with assay types and experimental design.
- Working with frozen or fixed samples, such as single-nuclei sequencing and snPATHO-seq.
- New sequencing modalities, highlighted by the VIB core facilities. We will provide an inside look at what happens during library preparations in the core facilities.
- Our progression towards long-read single cell sequencing and sequencing-based spatial transcriptomics.
Our guest keynote speaker, Assistant Professor Christoph Ziegenhain from the Karolinska Institutet, will share his experiences on how his lab is generating and adopting new single cell sequencing methods.
In the next three days we go through the whole analysis pipeline but this part is already full. We will teach you how to:
- get the data into R
- do proper quality control and filtering on gene level and cell level
- cluster the cells and create UMAP plots
- find potential markers for a subset of cells or genes that are differentially expressed between conditions
- further downstream analyses will be catered according to the participants needs
There will be room to start the analysis of your own data under the supervision of experts.
This part of the summer school is already full, you can no longer register for it.
Trainers
Christoph Ziegenhain
Christoph Ziegenhain worked on emerging single-cell sequencing technologies and evolutionary genomics. Currently, he is assistant professor and group leader at Karolinska Institutet and his research focusses on regulation of alternative splicing at single cell resolution. Christoph is also CEO of Xpress Genomics, a sequencing technology company committed to providing highest quality single cell RNA sequencing tools.
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.
Evelien Van Hamme
Evelien Van Hamme leads the Spatial Catalyst team in VIB. She obtained her PhD in 2009 at the university of Ghent studying viral entry of coronaviruses in monocytes. She has 12 years of experience in advanced bio imaging applications such as live cell imaging, functional imaging and CLEM workflows. In 2018 her interest in spatial technologies was raised when she started evaluating the Akoya CODEX technology. Since 2023 she focuses on spatial technology applications in life science research together with a team of data analysts.
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.
Janick Mathys
Janick tries to help VIB scientists analyze their data by offering bioinformatics training and support. Next to organizing trainings, creating e-learning courses and teaching statistics, R, Python, Linux, HPC, bulk and single cell RNA-Seq analysis, she consults scientists and develops pipelines for omics analyses. Before joining VIB, she worked as a post-doc at KULeuven, doing research on transcriptomics and transcription regulation. She coordinated the Master of Bioinformatics program of KULeuven and taught the course on Biological Databases.
Program
9h-9h30 Arrival and coffee
9h30-10h30 scRNAseq concepts and platforms (Niels Vandamme)
10h30-11h Coffee break
11h-12h scRNAseq assays and sample types (Niels Vandamme and Ria Roelandt)
12h-13h Lunch
13h-13h30 Plate-based single-cell assays (Thomas Eekhout)
13h30-14h15 Scalable full-length single-cell RNA-seq to decode alternative mRNA splicing (Christoph Ziegenhain)
14h15-14h45 Long-read single-cell sequencing (Robin Boiy)
14h45-15h15 Coffee Break
15h15-16h15 Introduction to sequencing platforms (Stefaan Derveaux and Element Biosciences)
16h15-17h00 Combining single cell and spatial data (Niels Vandamme and Evelien Van Hamme)
9h30-10h15 Experiment design and multiplexing strategies (Niels Vandamme)
10h15-10h30 Coffee break
10h30-12h Interpretation of quality control reports (Niels Vandamme and Ria Roelandt)
12h-13h Lunch
13h-17h30 Hands on: Data import, QC and clustering (Janick Mathys)
9h30-12h30 Hands-on: Annotation, batch correction and DGE (Janick Mathys)
12h30-13h30 Lunch
13h30-17h Hands-on: Data mining tools (content decided by participants)
9h30-16h DIY: Analysis of own data under supervision of experts
9h30-10h30 Meet the expert: scATAC-Seq analysis
10h30-11h30 Meet the expert: cell-cell communication
Practical info
09 September 2024
Ghent - VIB/UGent FSVM I
Technologiepark 71
9052 Zwijnaarde
Belgium
10 September 2024 - 12 September 2024
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
09 September 2024
Ghent - VIB/UGent FSVM I
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
10 September 2024 - 12 September 2024
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
09 September 2024
Ghent - VIB/UGent FSVM I
Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
Shared bicycles
Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic
There are also some public bicycle pumps at the park.
10 September 2024 - 12 September 2024
Ghent - VIB/UGent FSVM II
Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
Shared bicycles:
Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic
There are also some public bicycle pumps at the park.
09 September 2024
Ghent - VIB/UGent FSVM I
There is only one entrance to Technologiepark. At the entrance, please take a ticket - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.
10 September 2024 - 12 September 2024
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.
09 September 2024
Ghent - VIB/UGent FSVM I
+32 9 331 36 00