This Document Resource includes links to documentation and how-to video series that can be used prior to getting started and while performing a Visium CytAssist Spatial Gene Expression for FFPE experiment.

Visium CytAssist Spatial Gene Expression for FFPE Document Resources

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

CytAssist Spatial Gene Expression analyzes the whole transcriptome of FFPE, Fresh Frozen, or Fixed Frozen tissue sections in a spatially resolved manner

Documentation for Fresh Frozen and Fixed Frozen Applications.

Frozen Tissue Applications

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

Tissue Prep

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.

Library Construction

Refer to instrument-specific documents for seamless instrument operation.

Instruments

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

CytAssist Spatial Gene Expression

Overview

User Guides

Workflow Documentation

Additional Applications

Datasets

Videos: CytAssist - FFPE

Videos: CytAssist - Frozen

Publications

A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data.

What is CytAssist Spatial Gene Expression?

CytAssist Spatial Gene Expression analyzes the whole transcriptome of FFPE, Fresh Frozen, or Fixed Frozen tissue sections in a spatially resolved manner by mapping gene expression over a high resolution microscope image of the tissue.

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

CytAssist Spatial Gene Expression for Fresh Frozen

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

CytAssist Spatial Gene Expression for Fixed Frozen

Find resources, from protocols to free-to-use analysis tools for processing human or mouse FFPE, Fresh Frozen, and Fixed Frozen tissues.

Documentation

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

Videos - CytAssist Spatial Gene Expression

Visium CytAssist Instrument

Tissue Preparation Guide

Deparaffinization, H&E Staining, Imaging & Decrosslinking

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 FFPE Document Resources

Getting Started, CG000641

CG000641_Document Resources_VisiumCytAssistSpatialProtocols_RevA.pdf