10x Genomics Logo

What is Visium?

The Visium platform, developed by 10x Genomics, enables the profiling of the entire transcriptome of fresh and formalin fixed paraffin-embedded (FFPE) tissues. FFPE preservation can damage RNA, posing a challenge for transcriptomic research. However, Visium Spatial Gene Expression for FFPE overcomes this obstacle by providing high-resolution and sensitive spatial profiling of the entire transcriptome of human FFPE tissue sections. Moreover, Visium for FFPE is compatible with IF and allows for protein co-detection in addition to H&E staining.

The Visium Spatial Gene Expression method is utilized in genomics research to investigate the patterns of gene expression in tissues, taking into account their spatial information. The procedure involves using a slide-based platform to capture the spatial organization of RNA molecules within the tissue.

Initially, tissue sections are secured onto a slide and then treated to maintain the RNA molecules' original positions. Following this, barcoded oligonucleotides are introduced to the tissue sections, which attach to the RNA molecules and enable their identification during sequencing.

Once the tissue sections are ready, the RNA molecules undergo sequencing. The data obtained is then analyzed to ascertain the gene expression levels and their spatial distribution within the tissue. This knowledge can offer valuable insights into different biological processes, including tissue development, cellular interactions, and disease pathology.

H&E Staining

H&E Staining

Visium Total UMIs

Visium Total UMIs

Visium Total Genes

Visium Total Genes

How Does Visium Work?

How Does Visium Work? Spatial LifeStrands

The Visium Spatial Gene Expression for FFPE workflow measures RNA levels in intact, formalin-fixed paraffin-embedded (FFPE) tissue sections, using probes targeting the whole transcriptome.

Visium gene expression slide is covered with spatial spots which contains location information.

Spatial primers are attached to gene targeting probes in the elongation step. Thus, merging expression and spatial information

Those elongated sequences are read by next generation sequencing and map back to their original spots.

Initial H&E and IF stainings could be merged with spatial transcriptomics results using the Space Ranger-Data Visualization tool.

Space Ranger counts oligo ligation events to build the feature-barcode matrix.

As a consequence, if the probe is hybridized to a transcript with a variant, that variant will not be present in the sequencing data. The probe design avoids known SNPs.

Why Choose 10x Genomics

The use of 10x Genomics technology permits researchers to conduct high-resolution genomic analysis, which facilitates the examination of intricate biological systems and the discovery of previously concealed information regarding cellular behavior and function.

With the provision of advanced tools and technologies, 10x Genomics seeks to expedite scientific breakthroughs and reveal fresh perspectives on human health, disease mechanisms, and other biological phenomena.

Turnkey
Solution

It is easy to integrate into your research as all the necessary reagents are included in the kit and no specialized equipment is required. This method is versatile and can be used with various sample types such as FFPE and fresh frozen, and different species including human, mouse, rat, and others.

Beyond gene
expression

Layer transcriptome and proteome data onto your stained images to understand tissue microenvironments like never before. Reveal the spatial organization of newly discovered cell types, states and biomarkers.

Easily Adoptable
Workflow

Integrate easily with your current laboratory methods and tools for tissue analysis. By combining it with immunofluorescence staining and imaging, you can obtain comprehensive characterization of multiple topics within the spatial context.

Streamlined Data
Analysis

Utilize Space Ranger analysis software to examine and comprehend the diversity in gene protein expression, followed by interactive exploration of the outcomes through Loupe Browser visualization software.

Work Flow of our Services

Kick-off Meeting

Prepare target

Discuss feasibility of the project

Prepare charged slide for the experiment
Spatial LifeStrands 13

Preliminary Service

H&E Staining

Mock Immunofluorescence Staining (IF)

DV200 (Checking for RNA quality of sample)

Mock ROI selection (to visualize cell count)
Spatial LifeStrands 13

Visium Days

Slides would be hybridized with probes and stained with H&E or IF.
Spatial LifeStrands 12

Analysis

Space ranger and Loupe browser for data analysis

Easily generate heatmaps, violin plots and spatial maps
Spatial LifeStrands 11

Validation

Using single cell confirmation by RNAscope ISH

Our Other Technologies

Spatial LifeStrands 8

Nanostring (GeoMx)

NanoString's GeoMx Digital Spatial Profiler (DSP) is a technology that enables comprehensive spatial and molecular analysis of RNA and protein in tissue samples on glass slides.
CosMx SMI

Nanostring (CosMx)

CosMx SMI is the first high-plex in situ analysis platform to provide spatial multiomics with formalin-fixed paraffin-embedded (FFPE) and fresh frozen (FF) tissue samples at cellular and subcellular resolution.

Find Out More About our Services.