Break through the barriers that once hindered spatial analysis of gene expression in formalin-fixed paraffin-embedded (FFPE) tissue sections and unveil the hidden insights within your samples with Visium Spatial Gene Expression for FFPE. By merging the advantages of histological techniques with the vast throughput and investigative capabilities of RNA sequencing in FFPE tissue samples, Visium Spatial Gene Expression for FFPE enhances traditional pathologist-led analysis. Profile RNA expression across entire tissue sections with high resolution, encompassing more than 18,000 genes in human and mouse FFPE samples, to gain spatial insight into gene expression patterns.
Visium HD empowers a new era of spatial discovery, enhancing proven whole transcriptome spatial analysis with single cell–scale resolution, enabling continuous tissue coverage, and delivering best-in-class data with innovative probe-based chemistry and a Visium CytAssist-enabled workflow.
Applications
Cancer Research: Comprehensive cellular maps of FFPE tumor sections, including benchmarking data from Visium HD and Visium v2 in normal adjacent tissues, providing insights into tumor heterogeneity and immune evasion mechanisms
Neuroscience: Create high-resolution maps of gene expression in the brain, helping to understand the spatial organization of different neuronal and glial cell types.
Immunology: By mapping the spatial distribution of immune cells within tissues, researchers can study immune cell interactions, migration, and their roles in immune responses.
Sample Requirements
| Sample Type | Sample Amount | Preservation | Sample QC | Shipping |
| FFPE block (recommended) |
1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device |
After embedding store at 4°C, protected from light |
DV200% ≥ 30% | 4°C or Room Temperature |
| FFPE slide | 5-10 FFPE (10μm thickness) scrolls in tube for sample QC； 2-4 FFPE (5μm thickness) tissue sections on glass slides, for library prep* |
Dry and sealed, storage time at 4°C < 14 days |
DV200% ≥ 30% | 4°C or Room Temperature |
*FFPE glass slides must be positive charged glass slides.
Specifications: Sequencing and Analysis
| Visium CytAssist (V2) | Visium HD | |
| Species | Human or mouse | Human or mouse |
| Resolution | 55 um | 2 um (single cell level) |
| Sequencing platform | Novaseq6000 or NovaSeq X plus | Novaseq6000 or NovaSeq X plus |
| Read length | PE150 | PE150 |
| Recommended Data Amount | 25,000 read pairs/ tissue-covered spot~ 50 Gb/sample | Coverage Area x 275,000,000 read pairs~ 100 Gb/sample |
| Analysis | Data QC
Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG) DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment |
|
Project Workflow
