University of Michigan Single Cell Sequencing | Spatial Analysis Resources



Spatial:10x Genomics Visium & Xenium, Nanostring GeoMx Digital Spatial Profiler, Curio Bioscience Curio Seeker & Curio Trekker. Single-cell: 10x Genomics, Parse Biosciences, Direct Cell Lysis, Mission Bio

Microscopes: Widefield, Confocal, Multiphoton, Superresolution, Lightsheet, Electron (SEM & TEM)
Services: consultation, image analysis, EM & LM sample prep.

Bulk and single-cell electrostatic sorting and analysis (numerous platforms)
Microfluidic cell sorting via Miltenyi Tyto
Image-based spectral cell sorting on BD FACSDiscover S8 Conventional and Spectral workflows

Single-cell RNA-Seq: cell type clustering
Single-cell ATAC-Seq: psuedotime analysis, differential expression, reporter gene expression, functional enrichment

Quantitative LC-MS analysis of molecules and mass spectrometry imaging of spatial localization biomarkers in tissue section.
Preclinical ADME and pharmacokinetics for lead compound optimization in drug discovery and development. Clinical pharmacokinetics and dosage regimen design for clinical trials

Suspension CyTOF for 40-color flow cytometry analysis of single cells. Tissue CyTOF for 40-color imaging analysis of FFPE slides. Single cell data analysis and visualization – tSNE, UMAP, image overlay, and statistics. Antibody panels for both human and mouse samples. Sample staining and custom antibody conjugation. Discount available for core RCC members.

Sample processing, embedding, microtomy, frozen section, special staining, IHC/multiplex IHC/ISH (Ventana Discovery) and whole slide IF/BF scanning ( Akoya PhenoImager)

Data processing – normalization, quality control, batch effect correction. Data Visualization – UMAP, TSNE. Statistical analysis and pipeline development – identification of spatially variable genes, quantification of spatial cellular interactions/colocalization, spatial clustering, association with patient/clinical outcomes. Methods innovation – multi-sample analysis, data integration, spatial gene regulatory networks

Three Raman microscopes with laser wavelengths of 785, 633, 532, and 405 nm. Sub-micrometer spatial resolution hyperspectral mapping. Variable temperature and environmental control during sample analysis. Advanced chemometrics for data analysis.

PhenoCycler™-Fusion system enables ultrahigh-plex spatial phenotyping of whole slides at single-cell resolution with automated fluidics and iterative imaging

Spatial: spatial ATAC/Cut&Tag platform
Single-cell: single-cell methylation assay, nuclei prep (Tyto) for SC assays (with AGC)

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