Spatialomics
Requesting Training & Services
If you are interested in Spatialomic services please submit a UMN Spatialomics Project Interest Form to get started. A member of the UMN Spatialomics team will be in touch to discuss your project.
A Collaborative Frontier
University of Minnesota Spatialomic services are partnership between the University Imaging Centers (UIC) and the University of Minnesota Genomics Centers (UMGC).Together, we work in concert to provide new avenues for researchers to increase their understanding of cells in their morphological context. The relationship between cells and their relative locations within a tissue sample can be critical to understanding disease pathology. Spatialomics allows scientists to measure all the gene activity in a tissue sample and map where the activity is occurring. Already this technology is leading to new discoveries that will prove instrumental in helping scientists gain a better understanding of biological processes and disease.
Spatialomic Technologies
GeoMx Digital Spatial Profiler
Technology Overview
Bruker's GeoMx Digital Spatial Profiler (DSP) combines standard immunofluorescence techniques with digital optical barcoding technology to perform highly multiplexed, spatially resolved profiling experiments. In a single reaction, the DSP technology performs whole slide imaging with up to four fluorescent stains to capture tissue morphology and select regions of interest for high plex profiling. The DSP chemistry enables spatially resolved high plex profiling of RNA and protein targets on just two serial sample sections, with no-destructive tissue processing.
-
Minimum sample: protein or RNA analysis from formalin-fixed paraffin-embedded (FFPE) or fresh-frozen section
-
Morphological context: whole-slide 4 color imaging to guide profiling
-
Digital quantitation: up to 6 logs (base 10) dynamic range
-
Preserve precious samples with non-destructive processing
The GeoMx DSP is designed to fit into a range of research and plex needs, including applications in oncology, immunology, neuroscience, and developmental biology. For more information on available RNA and protein assays, as well as the Whole Transcriptome Atlas, visit Bruker's website.
Workflow
The GeoMx DSP Service is supported by the collaborative efforts of three core facilities at the University of Minnesota: UIC, CTSI Histology, and the UMGC.
- The Clinical and Translation Science Institute (CTSI) histology team provides optional assistance with tissue sectioning and mounting of FFPE or fresh frozen tissue.
- University Imaging Center (UIC) stains tissue slides with pre-mixed biological probes and fluorescently-labeled markers, works with investigators on ROI selection, and uses UV exposure to release DSP barcode tags from ROI. The UIC also provides consultation on the GeoMX DSP technology and assists with experimental design.
- UMN Genomics Center (UMGC) quantifies released tags on the nCounter or on an Illumina next-generation sequencer and counts are mapped back to tissue location to yield a digital profile.
The UIC and UMGC are neighboring facilities located at 1-220 and 1-210 Cancer & Cardiovascular Research Building (CCRB).
Pricing
Project costs for GeoMx DSP include services from multiple core facilities. Each core will provide an independent estimate and invoice for their portion of the service. The UIC and UMGC provide general pricing information on their websites.
Data Delivery
More information on GeoMx DSP data delivery can be found on the UMGC's GeoMx DSP webpage under "Guidelines".
CosMx Spatial Molecular Imager
Technology Overview
The CosMx Spatial Molecular Imager (SMI) is a high-plex in situ analysis platform providing spatial multiomics with formalin-fixed paraffin-embedded (FFPE) and fresh frozen (FF) tissue samples at cellular and subcellular resolution. CosMx SMI enables rapid quantification and visualization of up to 1,000 RNA and 64 validated protein analytes.
CosMx Spatial Molecular Imager is a robust spatial single-cell imaging platform for:
- Minimum sample: protein or RNA analysis from formalin-fixed paraffin-embedded (FFPE) or fresh-frozen section
- Defining cell types, cell states, tissue microenvironment phenotypes, and gene expression networks
- Understanding biological process controlled by ligand-receptor interactions
- Quantifying change in gene expression based on treatment and identify single-cell subcellular biomarkers
- Preserve precious samples with non-destructive processing
The CosMx SMI is designed to fit into a range of research and plex needs, including applications in oncology, neuroscience, infectious disease, immunology, and developmental biology. For more information on available RNA and protein assays, as well as available panels, visit Bruker's website.
Pricing
UIC CosMx SMI rates can be found on our rates page under the Spatialomic Services category.
Data Delivery
The UIC has three options for transferring data from the UIC to clients: 1) delivery to the Minnesota Supercomputing Institute’s (MSI) high-performance file system, 2) download with Globus or Box Secure Storage, or 3) shipment on an external hard drive. Data delivery will be discussed during the experimental design part of the project workflow.
1. MSI storage
UMN researchers will have their data delivered in the "data_delivery" folder in your group's folder on MSI's primary filesystem (home/GROUP/data_delivery/uic/cosmx_smi).
2. Globus and Box Secure Storage
Internal and External clients can use Globus or Box Secure Storage to download their data. These are the recommended method for external clients to download large datasets.
3. Hard drive
Clients may provide a hard drive to the UIC.
MIBIscope
Technology Overview
The MIBIscope System is a revolutionary imaging platform, enabling comprehensive phenotypic profiling and spatial analysis of the tissue microenvironment. The MIBIscope allows researchers to visualize over 40 markers simultaneously with higher sensitivity, resolution, and throughput than existing methods.
MIBI Technology is based on secondary ion mass spectrometry or SIMS. With SIMS, a primary ion beam is rastered across the surface of a sample, liberating reporter ions that are then simultaneously recorded on a pixel-by-pixel basis by Time-of-Flight detection. An ion beam, unlike a laser, enables resolution to be tuned over a broad range—in the case of the MIBIScope, from a few hundred nanometers to 1 micron. Once liberated, the reporter ions, or “secondary ions,” travel uninterrupted at supersonic speed from the sample to the detector, leading to fast acquisition and extraordinary sensitivity.
Pricing
UIC MIBIscope rates can be found on our rates page under the Spatialomic Services category.