Best practices for handling FFPE tissue samples and slides before and after sectioning. Guidance for removing hardset coverslips from archived tissue slides.

Tissue Prep

### What is CytAssist Spatial Gene Expression for Fresh Frozen (FF)?

W﻿hole transcriptome analysis of mouse or human fresh frozen OCT embedded tissue sections utilizing probe-based chemistry.

T﻿his assay utilizes the following 10x products:

* V﻿isium CytAssist Spatial Gene Expression for FFPE Reagent Kits
* Visium CytAssist Instrument and Accessory Kit, to learn more [click here](/instruments/visium-cytassist)

T﻿his assay has been validated with the following:

* Fresh frozen OCT embedded tissue blocks 
* 10-20 µm section thickness
* H&E Staining
* Tissue types ([Tested Tissue List](/support/cytassist-spatial-gene-expression/documentation/steps/experimental-design-and-planning/visium-cytassist-spatial-gene-expression-for-fresh-frozen-tested-tissue-list))

### 10x Visium Kit Compatibility Table

| Capture Method                           | 10x Solution                                                                                     | FFPE Tissue | Fresh Frozen Tissue | Fixed Frozen Tissue |
| ---------------------------------------- | ------------------------------------------------------------------------------------------------ | ----------- | ------------------- | ------------------- |
| CytAssist-enabled, Probe-based chemistry | [Visium CytAssist Spatial Gene Expression](/support/spatial-gene-expression-ffpe)                | <Check />   | <Check />           | <Check />           |
| Direct Placement, Probe-based chemistry  | [Visium Spatial Gene Expression for FFPE](/support/spatial-gene-expression-ffpe)                 | <Check />   | \-                  | \-                  |
| Direct Placement, Poly-A based chemistry | [Visium Spatial Gene Expression for Fresh Frozen](/support/spatial-gene-expression-fresh-frozen) | \-          | <Check />           | \-                  |

Whole transcriptome analysis of fresh frozen tissue sections utilizing probe-based chemistry.

CytAssist Spatial Gene Expression for Fresh Frozen

Visium CytAssist Instrument facilitates the transfer of analytes from standard glass slides to Visium slides. Find the Instrument Documentation via the button below.

Visium CytAssist Instrument

Visium CytAssist Spatial Gene Expression User Guide

### What is CytAssist Spatial Gene Expression for Fixed Frozen (FxF)?

W﻿hole transcriptome analysis of mouse fixed frozen OCT embedded tissue sections utilizing probe-based chemistry.

T﻿his assay utilizes the following 10x products:

* V﻿isium CytAssist Spatial Gene Expression for FFPE Reagent Kits
* Visium CytAssist Instrument and Accessory Kit, to learn more [click here](/instruments/visium-cytassist)

T﻿his assay has been validated with the following:

* Paraformaldehyde (PFA) fixed, sucrose cryopreserved, OCT embedded tissue blocks
* 10-20 µm section thickness
* H&E Staining
* Tissue types ([Tested Tissue List](/support/cytassist-spatial-gene-expression/documentation/steps/experimental-design-and-planning/visium-cytassist-spatial-gene-expression-for-fixed-frozen-tested-tissue-list))

### 10x Visium Kit Compatibility Table

| Analyte Capture Method                   | 10x Solution                                                                                     | FFPE Tissue | Fresh Frozen Tissue | Fixed Frozen Tissue |
| ---------------------------------------- | ------------------------------------------------------------------------------------------------ | ----------- | ------------------- | ------------------- |
| CytAssist Enabled, Probe-based chemistry | [Visium CytAssist Spatial Gene Expression](/support/spatial-gene-expression-ffpe)                | <Check />   | <Check />           | <Check />           |
| Direct Placement, Probe-based chemistry  | [Visium Spatial Gene Expression for FFPE](/support/spatial-gene-expression-ffpe)                 | <Check />   | \-                  | \-                  |
| Direct Placement, Poly-A based chemistry | [Visium Spatial Gene Expression for Fresh Frozen](/support/spatial-gene-expression-fresh-frozen) | \-          | <Check />           | \-                  |

Whole transcriptome analysis of fixed frozen tissue sections utilizing probe-based chemistry.

CytAssist Spatial Gene Expression for Fixed Frozen

Additional Applications

Documentation for Fresh Frozen and Fixed Frozen Applications.

Frozen Tissue Applications

Plan ahead by referring to the list of equipment, kits, and reagents needed for the Visium CytAssist Spatial Gene Expression protocols.

Experimental Design

Experimental Planning & Design

Deparaffinize, stain, image, and decrosslink FFPE tissue sections.

Tissue Staining

For imaging hardware, general image acquisition and analysis guidelines, and example images.

Imaging

Find a list of probes targeting protein-coding genes in human or mouse transcriptome for the Visium CytAssist Spatial Gene Expression assay.

Probe Sets

Construct a sequencing-ready Visium spatial library from your FFPE tissue sections.