What platform is right for me?
| Platform | 10X Genomics Visium | 10X Genomics Xenium | NanoString GeoMx DSP |
| Sample Type | Fresh Frozen, Fixed Frozen, or FFPE | Fresh Frozen, Fixed Frozen, or FFPE | Fresh Frozen, Fixed Frozen, or FFPE |
| *Submission Format | All samples require an annotated H&E, blocks, glass slides, or 10x custom slides | All samples require an annotated H&E; blocks or 10x custom slides | blocks or standard slides (freshly cut) |
| **Recommended QC | Manual FF RIN >7; CytAssist or HD DV200 > 30% | Tissue: H&E and DAPI stain, RNA: DV200 >30% | none |
| Capture Area | Manual FF: 6.5 mm x 6.5 mm (2 per slide) | 10.45 mm x 22.45 mm | up to 40 x 17 mm |
| CytAssist: 6.5 mm x 6.5 mm or 11mm x 11mm (2 per slide); HD: 6.5 mm x 6.5 mm | |||
| Species | Manual: diverse; CytAssist or HD: human or mouse | diverse | human or mouse |
| Analyte | Manual FF: RNA, CytAssist: RNA and protein; HD: RNA | predesigned or custom targeted RNA panels | RNA or protein |
| Resolution | Manual or CytAssist: 55um spots; HD: 8um bins (can be parsed into 2um) | subcellular | minimum 50-100 cells per ROI |
| Visualization | H&E or immunofluorescence | H&E or immunofluorescence (post Xenium processing) | four-color fluorescence |
| Core Deliverables | SpaceRanger analysis pipeline output | Xenium pipeline output | Quality Control Report with R objects |
| ***Downstream Analysis: Available but NOT provided by the Core | Loupe Browser Visualization Software and 3rd party tools (e.g., Seurat) | Xenium Browser Visualization Software and 3rd party tools (e.g., Seurat) | vendor supplied R packages |
*Please reach out to Kate Smith, smithkm13@upmc.edu, for information on sample submission.
**Please reach out to hccr-cgfcorelab@pitt.edu for information on RNA extraction and QC.
***Downstream analysis is not provided, please reach out to staff for recommendations.
