Provides step-by-step guidance for deparaffinization, Hematoxylin & Eosin (H&E) staining, imaging, and decrosslinking of tissue for use with 10x Genomics Visium CytAssist Spatial Gene Expression for Fresh Frozen assay.

Visium CytAssist Spatial Gene Expression for Fresh Frozen – Methanol Fixation, H&E Staining, Imaging & Destaining

Deparaffinize, stain, image, and decrosslink tissue.

Tissue Staining

Visium Spatial Gene Expression measures the whole transcriptome of FFPE tissue sections in a spatially resolved manner by mapping gene expression over a high-resolution microscope image of the H&E- or IF-stained tissue.

CytAssist for FFPE

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

Experimental Design

Experimental Planning & Design

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

Tissue Prep

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 for FFPE assay.

Probe Sets

Refer to instrument-specific documents for seamless instrument operation.

Instruments

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

Library Construction

Sequence your Visium spatial library as per our provided recommendations.

Sequencing

Analyze your Visium spatial data using our pipelines and visualization tools.

Software Analysis

Visium CytAssist Spatial Gene Expression for FFPE

FFPE

Experimental Planning and Design

For proper FFPE tissue sectioning and placement.

Visium Spatial Gene Expression for FFPE

Visium CytAssist

Spatial Gene Expression

Overview

Documentation

Additional Applications

Datasets

Videos-CytAssist for FFPE

Videos-FFPE

Publications

Spatial Gene Expression for FFPE

Visium Spatial Gene Expression analyzes the whole transcriptome of FFPE tissue sections in a spatially resolved manner by mapping gene expression over a high-resolution microscope image of the tissue.

What is Spatial Gene Expression for FFPE?

CytAssist-enabled whole transcriptome analysis of fresh frozen tissue sections utilizing probe-based chemistry.

CytAssist Spatial Gene Expression for Fresh Frozen

Find resources, from protocols to free-to-use analysis tools.

Access free, publicly available data from a number of different sample types generated with Visium Spatial solutions

Videos - Visium CytAssist Spatial Gene Expression for FFPE

Visium CytAssist Instrument Tour and Readiness Test

Tissue Preparation Guide

Deparaffinization, H&E Staining, Imaging & Decrosslinking

Videos - Visium Spatial Gene Expression for FFPE

Visium Spatial Gene Expression for FFPE Protocol

Visium Spatial Gene Expression for FFPE Tissue Preparation Guide

Find answers to common technical questions, from sample prep through data analysis, about Visium spatial workflows.

Read key peer-reviewed research publications offering greater insights into biology, enabled by 10x Genomics products and technologies.

Visium CytAssist Spatial Gene Expression for Fresh Frozen – Methanol Fixation, H&E Staining, Imaging & Destaining

Demonstrated Protocol, CG000614

CG000614_Demonstrated_Protocol_VisiumCytAssist_FreshFrozen_H&E_RevA.pdf