The Next Generation Sequencing Competence Network (NGS-CN), an initiative funded by the Deutsche Forschungsgemeinschaft (DFG), is proud to announce its 5th Summer School! taking place in May 2025. This round the course will focus on training young researchers in the cutting-edge field of spatial transcriptomics (with some content on single cell transcriptomics).
The aim of this school is to introduce students to the field of spatial omics, focusing on Spatially Resolved Transcriptomics (SRT). SRT technologies, which have shown an exponential growth in recent years, allow unprecedented detection of spatial organization of gene expression within tissue context leading to new understandings of biological questions.
NGS-CN Summer School Logo was created by Juliana Roscito.
Data images are kindly provided by Kenneth Peuker and Julieta Aprea.
Program
Hybrid Module
Hands-On Module
The hybrid module is designed to provide an extensive overview of single-cell and spatial transcriptomics technologies, offering both foundational knowledge and advanced insights into their applications.
Throughout this module, you will gain a deep understanding of the fundamental concepts and methodologies that drive spatial omics, with a focus on how these technologies can be used to study gene expression in individual cells and within tissue contexts. You will also learn when and why to utilize each approach, helping you make informed decisions about which method best suits your research objectives.
In addition to mastering the core principles of single-cell and spatial transcriptomics, you will be introduced to essential bioinformatics techniques used to analyze and interpret the vast amount of data generated by these technologies.
Special attention will be given to the integration of single-cell and spatial transcriptomic data, demonstrating how these combined approaches can yield richer insights into biological processes and disease mechanisms.
To further enrich the learning experience, the module includes a series of scientific talks delivered by leading experts in spatial transcriptomics. These talks will explore the latest advancements and real-world applications of these technologies across various research fields, showcasing their transformative potential in advancing our understanding of complex biological systems.
By the end of the module, you will be well-equipped with the knowledge and skills needed to apply single-cell and spatial transcriptomics in your own research projects. We look forward to meeting you!
The in-person module will consist of hands-on training on spatial transcriptomics, both for bench work and for bioinformatic analysis.
Bench
Understand and practice spatial transcriptomics workflows, using Visium HD from 10x Genomics as a case study.
In this section of the module you will obtain hands-on experience with the critical steps of spatial transcriptomics workflows, including sample quality control, histology, working with Visium slides, Gaskets, and Cytassist, as well as key protocol steps and qPCR analysis. We aim to enable you to properly design your experiment and prepare your samples, as well as set up this workflow in your laboratories.
Bioinformatics
You will learn how to analyze spatial transcriptomics data, starting from a pre-mapped counts table. This workshop will cover essential techniques like quality control, normalization, dimensionality reduction, clustering, and spatial visualization. Participants will work on their own laptops, equipped with a provided workbook and a software package. A team of instructors will be available throughout to offer one-on-one assistance and ensure you gain practical confidence in spatial transcriptomics analysis.
- Work with real-world spatial sequencing data
- Follow established workflows using R, Rstudio, Quarto, and Seurat
- Receive personalized support from our team of experts
- Take home a comprehensive workbook for continued learning