Agenda and Registration
Agenda
8:30 AM - Check-in and light refreshments (no breakfast)
9:00 AM - Welcome and intro, Kenny Beckman, PhD, UMGC Director
9:10 AM - Mike Farrar, PhD, Professor, Medicine, LMP
9:45 AM - Monica Campo Patino, PhD, Assistant Professor, Medicine, Pulmonary Division
10:20 AM - Coffee break
10:40 AM - Adam Herman, PhD, Bioinformatics Analyst, MSI
11:00 AM - Indrani Poddar, PhD, Postdoctoral Researcher (Mike Lee Lab), Neuroscience
11:20 AM - Jitu George, PhD, Single Cell Lead, UMGC
11:35 AM - Christine Henzler, PhD, MSI Co-Director of Research Informatics
11:50 AM - Questions and answers for the cores
12:00 PM - UMGC CoLab open house
12:30 PM - Adjourn
Registration
This event is for UMN researchers. Advanced registration is required for this in-person symposium, and there is no cost to attend.
Abstracts
My journey through scRNA-Seq: Riding the wave from hard and expensive to (relatively) easy and cheap
Mapping Innate Immune Heterogeneity in Human BALF Using scRNA-seq and Ex Vivo Infection Models
Monica Campo, MD, MPH, Assistant Professor, Pulmonary, Allergy, Critical Care and Sleep Medicine Division, Department of Medicine
Our lab focuses on the heterogeneity of the human innate immune response in chronic lung infections. We developed an ex vivo infection model using bronchoalveolar lavage fluid (BALF) cells from healthy volunteers to investigate early immune responses to mycobacterial challenge. BALF cells were infected with Mycobacterium bovis BCG and analyzed using single-cell RNA sequencing. We identified major BALF cell types and focused on eight alveolar macrophage clusters, with IFN and cytokine-enriched clusters showing the greatest transcriptional activation post-infection. Cluster proportions shifted significantly after BCG exposure, correlating with antimicrobial activity in vitro. This approach integrates primary human samples, controlled ex vivo infection, and high-resolution transcriptomics to dissect early lung innate responses and cellular heterogeneity, providing a framework for mechanistic studies of host-pathogen interactions in the human airway.
Sequencing a single-cell gene expression library with Oxford Nanopore
We will discuss our experience sequencing a 10X Genomics 5’ v3 GEX library with Oxford Nanopore Technologies (ONT) Promethion sequencer. We will compare and contrast these results with those generated from 10X 5’ v3 GEX + TCR library from the same sample sequenced on Element Biosciences AVITI platform. In particular, we’ll look at the full-length TCR sequences generated by ONT and the TCR sequences assembled from the short-read data by the cellranger software. Finally, we’ll also touch on the variant calling implemented in the ONT software package wf-single-cell.
Single nuclei sequencing of brain tissue – a CoLab experience
We are using Parse fixed single nuclei RNAseq method to map LAMDA (Lewy-associated
molecular dysfunction from aggregates) and senescence in mouse model of α-synucleinopathy.
We've successfully optimized this workflow at the UMGC CoLab to manage limited and
challenging samples. This collaborative environment proved invaluable, offering direct access to
instrumentation, hands-on training, and expert support for refining our protocols. I'll be
discussing my experience with the CoLab and sharing the results from our snRNAseq analysis.
The Future of Single-Cell RNA-Seq: Affordable and Scalable
Single-cell RNA sequencing enables detailed exploration of cellular heterogeneity and the
identification of rare cell populations. However, large-scale studies are often constrained by cost
and limitations in sequencing throughput. The UMGC will present the integration of 10X
Genomics and Parse library preparations with the Ultima sequencing platform, achieving high-
throughput sequencing at a significantly reduced cost per base—without compromising data
quality. We will also outline our plan to expand our single-cell services to include sample
preparation, allowing researchers to submit cryopreserved cells, frozen tissues, and OCT sections
for downstream workflows. As a demonstration, we will showcase results from where we isolated
nuclei from frozen tissue samples and processed them using the 10X Genomics and Parse
workflows.
Bioinformatic Challenges and Insights from 100+ Experiments
Christine Henzler, PhD, Minnesota Supercomputing Institute Co-Director of Research Informatics
Advances in sequencing technologies and single-cell library preparation techniques are allowing researchers to design more complex and bigger single-cell experiments than ever before. As researchers harness these new technologies to ask more nuanced questions or tackle biobank-scale projects, analysis techniques are also evolving, with ongoing algorithm development and benchmarking across the whole spectrum of single cell analysis, from QC and data cleaning, to clustering, cell typing, integration, differential expression, open chromatin analysis, TCR and BCR profiling, pseudotime, RNA velocity, and more. Our group has analyzed over 100 single-cell and single-nucleus experiments across a variety of technologies, library prep methods, species, and experimental designs. I will discuss current informatics challenges in the analysis of these data, lessons learned from our work, and our evolving experimental design and analysis guidelines. I’ll also highlight MSI resources available for researchers for single-cell data analysis.
Location and Parking
Location:
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.
Parking:
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.