Cutting-Edge Sequencing 101: The 5th NGS-CN Summer School on Spatial Transcriptomics Hosted in Dresden

In May, experts from the DRESDEN-concept Genome Center (DcGC) hosted the 5^th NGS-CN Summer School on Spatial Transcriptomics. This cutting-edge technology allows scientists to quantify and visualize gene expression of a large number of genes within tissue samples. More than 200 researchers attended the event both online and in person at the Center for Regenerative Therapies Dresden (CRTD). The summer school provided a thorough introduction to single-cell and spatial transcriptomics technologies and data analysis. The event was organized under the umbrella of the Next Generation Sequencing Competence Network (NGS-CN).

Spatial transcriptomics is a relatively new technology with the potential to revolutionize molecular biology. “It combines high-end sequencing with histology, allowing us to get not only which transcripts are expressed but also exactly where in the tissue, in some cases even at a single-cell resolution,” explains Dr. Julieta Aprea, the lead of the Spatial Omics unit at the DRESDEN-concept Genome Center (DcGC).

Although still relatively new, spatial transcriptomics is already well-established at the DcGC. The recent Summer School on Spatial Transcriptomics offered a chance to share this in-depth expertise with researchers from other universities and institutes all over the world.

Hybrid Approach

The first part of the Summer School was a hybrid event, allowing participants to join either online or in person in Dresden. Through a series of talks, around 200 attendees received practical insights on how to use spatial transcriptomics and how to analyze the resulting data. Talks from leading researchers rounded out the program, showcasing real-world applications of spatial transcriptomics.

“The hybrid format was a great networking opportunity. In a fast-evolving field like this, it is essential to build connections and learn directly from peers,” says Daniela Dey, Scientific Officer of the West German Genome Center WGGC.

Extensive Hands-On Training

The second part of the NGS-CN Summer School focused on hands-on training, with 16 early-career researchers getting a unique opportunity to learn the ins and outs of spatial transcriptomics. DcGC and NGS-CN experts and the CMCB Technology Platform gave detailed workshops covering each step of the experimental pipeline.

Susanne Weiche from the CMCB Histology Facility covered the essentials of sample preparation. Ellen Geibelt and Dr. Ruth Hans from the CMCB Light Microscopy Facility covered the high-throughput imaging of samples. Dr. Julieta Aprea, Sylvia Clausing, Annekathrin Kränkel, Dr. Neharika Chamachi, and Josefine Kleinert from the DcGC as well as Dr. Antje Becker from 10x Genomics guided the students through the VisiumHD workflow. Finally, Dr. Katrin Sameith-Lauber, Dr. Andreas Petzold, Dr. Ulrike Friedrich, Dr. Virag Sharma from the bioinformatics team of the DcGC and Dr. Joana Bernardes from the Competence Center for Genomic Analysis Kiel (CCGA) went through the data analysis pipeline and offered one-on-one guidance for the participants.

Funding and Organization

The NGS-CN Summer School on Spatial Transcriptomics was financially supported by the DFG-funded initiative the Next Generation Sequencing Competence Network (NGS-CN) as well as funding from DRESDEN-concept, Ministerium für Kultur und Wissenschaft NRW from the West German Genome Center (WGGC)  and commercial sponsors 10x Genomics, and Vizgen. This funding allowed the organizing team to provide travel and accommodation grants for 16 early-career researchers to benefit from the hands-on training.

The school was organized by the DcGC team in collaboration with the WGGC Scientific Officers Daniela Dey, Dr. Iuliia Novoselova, Dr. Anna-Maria Möller, and Dr. Martina van Uelft.