Which platform is right for you?
Spatial biology allows you to combine histology and RNA/protein analysis to capture the positional context of gene expression within intact tissue. The AFGC offers two platforms for spatial transcriptomics:
10X Visium and Nanostring GeoMx. Both platforms are discussed in greater detail below. Please contact us with any questions!
Platform | GeoMx DSP | 10X Genomics Visium |
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Sample Type | FFPE, Fresh or Fixed Frozen | FFPE, Fresh or Fixed Frozen |
Submission Format | Blocks or standard slides | Blocks or 10X Visium slide |
Recommended QC | None | FFPE DV200 |
Species | Human or Mouse | Fresh Frozen: Diverse, FFPE: Human or Mouse |
Analyte | RNA and/or protein | RNA |
Regions | Targeted - user defined (shape/size) regions of interest | 5000 spots per 6.5mm capture area, 14000 spots per 11mm capture area |
Slide area | up to 40 x 17 mm (can accommodate multiple sections) | 6.5 x 6.5 mm (4 per slide) |
Visualization | four-color fluorescence | H&E |
Deliverables | QC Report with R objects | SpaceRanger pipeline output |
Downstream Analysis | GeoMx visualization software, R analysis (vendor supplied packages and custom scripts) | Loupe Browser visualization software and 3rd party tools (e.g. Seurat) |
Summary
If you are interested in tissue heterogeneity and single cell resolution is important
- 10X Visium
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If you are interested in targeting specific regions/cell type within a large tissue area (ei. pancreatic islets)
- Nanostring GeoMx
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Contact us to discuss your project and decide which platform better suits your needs.
Nanostring GeoMx DSP
NanoString's GeoMx Digital Spatial Profiler (DSP) combines spatial and molecular profiling to generate whole transcriptome and/or protein expression for up to 4 tissue slides/day. Fluorescently tagged morphology markers are used to visualize the tissue and oligo-tagged profiling reagents are used to analyze RNA (probe) or protein (antibody). The power of the GeoMx platform is in the ability to select many user defined regions of interest (ROIs) based on the imaging results.
Starting a GeoMx Project
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The GeoMx DSP workflows are highly dependent on project and tissue type, therefore, projects require consultation and planning. The GeoMx DSP has the ability to profile the whole transcriptome and 150+ proteins targets from FFPE and fresh frozen tissue. The following topics will be discussed during the initial consultation along with your project goals and expectations:
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Arrangement of tissue sections on slides. The largest factor in the overall cost is the number of slides (max 4) because more oligo based reagents are needed. Multiple sections or sections from multiple blocks can be placed on the same slide within a large surface area as desired.
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Morphology markers. Choosing robust morphology markers is critical as they are used to guide the selection of ROIs and provide the ability to select specific cell types for collection. We can help you choose markers (up to three + nuclear stain) that are compatible with the GeoMx fluorescent channels.
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Imaging prior to DSP workflow. A dry run (mock probe hybridization) will be performed with all projects and scanned on the GeoMx DSP (without collection/library construction) to assess the morphology markers signal and ensure workflow conditions are suitable for your tissue type. We also recommend H&E staining serial sections. These images can help during the process of ROI and segmentation pattern definition.
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Process of defining ROIs. Investigators/research staff are heavily involved in ROI selection and must plan to be present for several hours on the date of the ROI collection. ROIs can be drawn in any shape, form concentric circles surrounding a landmark, or form a grid. You can select 1-96 ROIs per slide
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Services
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Whole Transcriptome Atlas
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Cancer Transcriptome Atlas
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Protein Assays with NGS readout
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Morphology marker optimization/validation
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A team of pathologists and histologists is available for consultation or embedding/sectioning and staining services.
We can also schedule a meeting with a Nanostring representative to address specific research questions.
10X Genomics Visium
The Visium platform combines histological information with unbiased whole transcriptome gene expression profiles using a Visium Gene Expression slide comprised of two or four capture areas. Capture areas contain 5000-14000 (depending on the slide) barcoded spots that are used to map gene expression data back to its location within the tissue. Each spot is ~55 um in size and covers 1-10 cells depending on tissue type. Spatial barcodes are incorporated during cDNA synthesis.
Starting a Visium Project
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The Visium platform has the ability to profile the whole transcriptome from an entire section from FFPE or fresh frozen tissue across multiple species. The following topics will be discussed during the initial consultation along with your project goals and expectations:
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Slide selection. A gene expression slide can feature either two or four capture areas. Standard capture area size is 6.5 x 6.5 mm and contains ~5000 spatial barcode spots.
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RNA quality of the tissue block. RNA quality must be assessed before beginning the Visium workflow. RIN scores should be >7. For FFPE (probe based) blocks the DV200 should be >50%, fresh frozen DV200 >30%.
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Coordination with tissue processing core. We work closely with the department of pathology at University Hospitals for tissue embedding, sectioning and staining.
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Services
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10X Visium (FF)
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10X Visium (FFPE)
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10X Visium Tissue Optimization
Consultation with our core staff is required before projects are accepted and is provided free-of-charge. Services listed include:
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consult to discuss research project and goals
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high quality images of full sections and regions of interest
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library preparation
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library QC using an Agilent Fragment Analyzer, Qubit 3 fluorometer and/or qPCR.
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We have a close partnership with the CWRU Genomics Core which operates a high-throughput sequencing facility.
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We also work closely a team of pathologists and histologists who can provide guidance when selecting regions of interest and assist with tissue embedding, sectioning, and H&E staining.