Spatial Transcriptomics

What Platform is Right For Me?

Sample Type: Fresh Frozen, Fixed Frozen, or FFPE
*Submission Format: All samples require an annotated H&E, blocks, glass slides, or 10x custom slides
**Recommended QC: Manual FF RIN >7; CytAssist or HD DV200 > 30%
Capture Area: Manual FF: 6.5 mm x 6.5 mm (2 per slide)
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
Analyte: Manual FF: RNA, CytAssist: RNA and protein; HD: RNA
Resolution: Manual or CytAssist: 55um spots; HD: 8um bins (can be parsed into 2um)
Visualization: H&E or immunofluorescence
Core Deliverables: SpaceRanger analysis pipeline output
***Downstream Analysis: Available but NOT provided by the Core: Loupe Browser Visualization Software and 3rd party tools (e.g., Seurat)

Sample Type: Fresh Frozen, Fixed Frozen, or FFPE
*Submission Format: All samples require an annotated H&E; blocks or 10x custom slides
**Recommended QC: Tissue: H&E and DAPI stain, RNA: DV200 >30%
Capture Area: 10.45 mm x 22.45 mm
Species: diverse
Analyte: predesigned or custom targeted RNA panels
Resolution: subcellular
Visualization: H&E or immunofluorescence (post Xenium processing)
Core Deliverables: Xenium pipeline output
***Downstream Analysis: Available but NOT provided by the Core: Xenium Browser Visualization Software and 3rd party tools (e.g., Seurat)

Sample Type: Fresh Frozen, Fixed Frozen, or FFPE
*Submission Format: blocks or standard slides (freshly cut)
**Recommended QC: none
Capture Area: up to 40 x 17 mm
Species: human or mouse
Analyte: RNA or protein
Resolution: minimum 50-100 cells per ROI
Visualization: four-color fluorescence
Core Deliverables: Quality Control Report with R objects
***Downstream Analysis: Available but NOT provided by the Core: vendor supplied R packages

Sample Type: Fresh Frozen or FFPE
*Submission Format: standard glass slides (freshly cut within 2 weeks)
**Recommended QC: GeoMx DSP data, DV200, RNAScope assay
Capture Area: 15 x 20 mm
Species: human or mouse
Analyte: RNA (custom targeted RNA panels) and protein. Also, simultaneous detection in the same tissue section
Resolution: Single-cell to subcellular (~500 nm pixel resolution)
Visualization: Multi-channel fluorescence imaging (4-color)
Core Deliverables: CosMx SMI Analysis output (cell segmentation, counts matrix, and visualization files)
***Downstream Analysis: Available but NOT provided by the Core: CosMx SMI Cell Analysis Software and compatible 3rd party tools (e.g., Seurat, Squidpy, Scanpy, python, R)

*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.