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
H&E Staining
How Does Visium Work?
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.
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
Preliminary Service
H&E Staining
Mock Immunofluorescence Staining (IF)
DV200 (Checking for RNA quality of sample)
Mock ROI selection (to visualize cell count)
Visium Days
Slides would be hybridized with probes and stained with H&E or IF.
Analysis
Space ranger and Loupe browser for data analysis
Easily generate heatmaps, violin plots and spatial maps
Validation
Using single cell confirmation by RNAscope ISH
Our Technologies
Nanostring (GeoMx)
