The Short Course on Spatial Transcriptomics

Spatial transcriptomics (ST) is a rapidly evolving field with great potential to shape our understanding of cells as actors in human health and disease by integrating cellular expression with position to illuminate the spatial organization of gene expression and inter-cellular communication. While ST technologies hold great promise for researchers, the complexity of the analytical methods creates a high entry barrier into the field, leaving researchers unable to take advantage of ST’s explanatory power. Some barriers to researchers seeking to adopt these technologies include insufficient access to in-person courses, lack of support in online tutorials, or a focus on less widely used technologies or programming languages. To train researchers to apply ST methods, we propose The Short Course on Spatial Transcriptomics at The Jackson Laboratory (JAX). This four-day course will focus on the fundamentals of ST technologies, applications, experimental design, and analysis of 10X Genomics Visium data in the R programming language, the most widely used technology and programming language in ST publications. The course will target researchers in neuroscience, cancer, development, genetics, and biomedical research at academic levels ranging broadly from graduate students to established researchers. Our goal is to build an educational program that recruits and cultivates new expertise, teaches rigorous, reproducible practices, and creates a nurturing climate and supportive network that builds a community while lowering barriers to entry into this rapidly emerging field. Achieving our goal will advance cutting-edge research at the Forefront of Genomics. While furthering NHGRI priorities, the proposed course will also promote rigorous, reproducible ST practices, create a collaborative network of ST practitioners, and deliver critical skills and practice for collaborative team training. Project Number: 1R25HG013926-01 | Fiscal Year: 2026 | NIH Institute/Center: National Human Genome Research Institute (NHGRI) | Principal Investigator: Gary Churchill | Institution: JACKSON LABORATORY, BAR HARBOR, ME | Award Amount: $155,269 | Activity Code: R25 | Study Section: Special Emphasis Panel[ZHG1 HGR-W (O1)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11015523