UMN Single Cell Symposium 2024

Tuesday, June 4
8:30 AM - 12:30 PM
1-125 CCRB

The field of single-cell genomics has progressed rapidly over the last 10 years and has changed the way we ask and answer biological questions. The ability to interrogate individual cells is revealing gene expression dynamics and cellular heterogeneity otherwise masked in bulk analysis. With the profiling of millions of cells in parallel, challenges arise in the experimental setup, the ability to limit errors and biases, and the analysis of vast quantities of data. 
This symposium aims to bring together UMN investigators interested in single-cell methods to discuss key approaches in data analysis and interpretation and the latest developments in single-cell technologies. It will feature in-depth presentations from UMN experts in cardiac, immunology, and plant research, updates in informatics approaches and single-cell technologies, and a tour of the new CoLab space for training in single-cell methods. 

This event is co-organized by the UMN Genomics Center and the Minnesota Supercomputing Institute. 

Topics to be covered include:

Single-cell genomics in immunology research
Single-cell genomics in cardiac research
Single-cell genomics in plant research
Single-cell informatics
Single-cell technologies

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Agenda and Registration


8:30 AM - Check-in and light refreshments (no breakfast)
9:00 AM - Welcome and intro, Christine Henzler, PhD, MSI Co-Director of Research Informatics
9:10 AM - Xavier Revelo, PhD, Associate Professor, Integrative Biology & Physiology and Center for Immunology
9:45 AM - Jop van Berlo, PhD, Associate Professor, Lillehei Heart Institute
10:20 AM - Coffee break
10:40 AM - Zachary Myers, PhD, Postdoctoral Researcher (Greenham Lab), Department of Plant and Microbial Biology
11:15 AM - Christine Henzler, PhD, MSI Co-Director of Research Informatics
11:35 AM - Kenny Beckman, PhD, UMN Genomics Center Director
12:00 PM - UMGC CoLab open house
12:30 PM - Adjourn


This event is for UMN researchers. Advanced registration is required for this in-person symposium, and there is no cost to attend. 

Register here


Single-cell genomics to study adaptive immune responses in metabolic disease

Xavier Revelo, PhD, Associate Professor, Integrative Biology & Physiology and Center for Immunology

Single-cell genomic technologies have revolutionized molecular biology by expanding our abilities to gain novel insights into inflammatory disease. Notably, inflammation plays a crucial role in the initiation and progression of metabolic disorders associated with obesity. However, our understanding of the mechanisms orchestrated by resident and infiltrating immune cells is limited. Using single-cell RNA and repertoire sequencing, we have discovered a bias towards aberrant inflammatory B and T helper subsets in the liver and gut-associated lymphoid tissues in a mouse model of disease. Overall, single-cell approaches at the interface of immunology and metabolism have been instrumental in identifying key mechanisms of metabolic disease.

Single-cell sequencing of cardiac cells using different platforms

Jop van Berlo, PhD, Associate Professor, Lillehei Heart Institute

The heart is a solid organ that contains cells that are too large for microfluidics-based strategies. Digestion protocols to release cells that are small enough for microfluidics platforms often result in extensive debris. Our experience with 3 different single-cell platforms will be shared along with insights and pros and cons for each.

Circadian cross-clock: using single-cell technologies to study rhythmic gene expression across cell types in plants

Zachary Myers, PhD, Postdoctoral Researcher (Greenham Lab), Department of Plant and Microbial Biology

The development and application of single-cell genomics approaches have enabled an unprecedented level of resolution to explore biology. While these techniques are of great interest to many plant biologists, they are often designed around and built with non-plant models in mind. Despite these challenges, the Greenham lab has begun adopting single-cell approaches to study circadian rhythms in gene expression at cellular resolution. In this presentation I will highlight how this level of resolution allows us to approach new questions surrounding cell-cell communication between oscillators, and will share key lessons learned along the way for researchers considering applying these approaches.

Leveraging the CoLab for single-cell genomics

Kenny Beckman, PhD, UMN Genomics Center Director

The UMGC CoLab is a new lab environment designed and equipped to help users succeed in complex genomic NGS workflows such as single-cell genomics (SCG). By providing specialized instrumentation, advanced training, and full 24/7 access, the CoLab enables faster turnaround, more affordable service, and convenience. We have begun acquiring cell isolation and purification devices and in June will begin the CoLab "Demo Days" program, in which not-yet-purchased devices will be placed in the core for extended periods for user "beta testing" in advance of a purchasing decision. Come hear about the S2 Genomics Singulator 200 (automated tissue disruption), the Miltenyi MACSQuant Tyto Cell Sorter (gentle cell sorting), the LevitasBio Levicell EOS (purification of viable cells and nuclei). All of these devices will be available starting in June, and will enable higher-quality SCG analysis using downstream workflows including 10X Genomics, Parse, and others.

Location and Parking

The Single Cell Symposium is hosted in the Cancer and Cardiovascular Research Building (2231 6th St SE, Minneapolis, MN 55455) located on the East Bank of the University of 
Minnesota. Check-in will be available at the main entrance. 

For parking near CCRB, we suggest parking in the Maroon and Victory daily lots ($6/day without in/out privileges) located across the street. 

Additional transportation options: 
The Metro Green Line (Light Rail) and select campus buses have stops near CCRB. A variety of detailed campus maps can help you navigate to CCRB.

About the Cores

UMN Genomics Center

The University of Minnesota Genomics Center (UMGC) provides genomic technologies and services to researchers and clinicians at the University of Minnesota, and to external academic and industry scientists throughout the United States and internationally. The UMGC acquires state-of-the-art instrumentation and offers an array of services, including next-generation sequencing, expression analysis, genotyping, single-cell and spatial genomics, metagenomics, and related support services such as nucleic acid extraction and quality control.

Minnesota Supercomputing Institute

The Minnesota Supercomputing Institute (MSI) provides advanced research computing infrastructure and expertise to the University of Minnesota research and scholarly community and the State of Minnesota in order to advance and accelerate research and foster innovation and discoveries through advanced computing technologies, scientific computing, and informatics, application development, and services.

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