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.
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
Dates
14. – 16.05.2025
Registration Deadline: 12.05.2025
19.-21.05.2025
Registration deadline: 02.03.2025
Sucessful applicants will be informed on: 17.03.2025
Cancellation deadline: 04.05.2025
Audience
This module is open to everyone who wants to learn about spatial transcriptomics
Life Sciences PhD students, Postdocs, and Master’s Students: Researchers with prior R knowledge who are currently working on or planning to start projects in spatial transcriptomics.
Bioinformaticians: Researchers preparing to work with spatial transcriptomics datasets and are interested as well in understanding “what is going on at the bench”.
Prerequisites
To ensure a smooth learning experience, participants are expected to meet the following requirements:
Hybrid Module: Participants are expected to join the Hybrid Module of the Summer School.
Interest in Spatial Transcriptomics: No prior experience with spatial sequencing is necessary, but familiarity with high-throughput sequencing concepts and RNA-seq will be required.
Basic R Knowledge: Familiarity with the R programming language, including running scripts and basic data manipulation, is essential to follow the course. To help participants prepare, we provide links to self-study resources below.
RStudio and R/Quarto Markdown: Familiarity with RStudio and R/Quarto Markdown is recommended. Participants will work with these tools during the workshop.
Laptop Preparedness: Bring your own laptop to the workshop. Please install the following software beforehand:
- Text editor, e.g. notepad++ on Windows, or vim on Mac and Linux
- SHH Client Putty on Windows to connect to our local HPC cluster
- Loupe Browser
All other required software and datasets will be provided in advance or at the beginning of the session.
Bioinformatics Self-Study for Preparation:
We ask all participants who are not already proficient in R to complete the free course available at https://swirlstats.com/students.html (“R Programming: The basics of programming in R”).
In addition, you can explore the following resources:
- RStudio Education: Beginner Resources
- Getting Started with Quarto in RStudio
- https://www.coursera.org/projects/getting-started-with-r
- https://www.codecademy.com/enrolled/courses/learn-r
This list is not exhaustive—there is plenty of excellent material available online to further support your learning.
Please note that participation is limited to individuals employed or/and conducting research in Germany and neighboring European countries, as the event is supported by national funding from DFG and MKW.NRW.
If you are unsure whether this applies to you, contact Daniela Dey (ddey [at] ukaachen [dot] de) for further details.
Venue and Accomodation
Online: Zoom (will be shared after registration)
In-Person: CRTD, Fetscherstraße 105, 01307 Dresden
Dresden-concept Genome Center (DcGC)
Fetscherstraße 105, 01307, Dresden
Accepted applicants are required to arrive in Dresden on 18.05. Accommodation will be provided from 18.-21.05, and catering will be provided from 19.-21.05.
The course will start on 19.05. at 8:30 am and end on 21.05. at 4:00 pm.
Transport grants will be provided based on the availability of funds.