8/6/23, 12:22 PM Spatial Transcriptomics - 10x Genomics

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Spatially resolved biology

Novel insights about

your tissue. Visualized.

Uncover the
"Where" for every
"What"
The relationship between cells and their relative locations
within tissue is critical to understanding normal
development and disease pathology. Spatial
transcriptomics is a groundbreaking molecular profiling
method that allows scientists to measure all the gene
activity in a tissue sample and map where the activity is
occurring. Already this technology is leading to new
discoveries that are proving instrumental in helping

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scientists gain a better understanding of biological

processes and disease.

Download Technology Brochure

How it works

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Fuel your spatial

discoveries with
spatial capture
technology
Spatial capture technology powers the Visium Spatial
platform through the use of spatially barcoded mRNA-
binding oligonucleotides. There are two methods for how
mRNA molecules get a spatial barcode.

In fresh frozen tissues, the tissue is fixed and permeabilized

to release RNA which binds to adjacent capture probes,
allowing for the capture of gene expression information.
cDNA is then synthesized from captured RNA and
sequencing libraries prepared.

In FFPE tissues, the tissue is permeabilized to release

ligated probe pairs that bind to adjacent capture probes on
the slide, allowing for the capture of gene expression
information. Pairs of probes specific to each gene in the
protein-coding transcriptome are hybridized to their gene
target and then ligated to one another. The probe pairs are
extended to incorporate complements of the spatial
barcodes and sequencing libraries prepared.

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Seminars

Examine gene
expression in the
context of the tissue
microenvironment
Innovation in spatial transcriptomics methodologies is
enabling scientists to get a holistic understanding of cells
in their morphological context. In this presentation, you will
hear first-hand from 10x Genomics scientists about
groundbreaking improvements to the technology and
exciting applications showcased by users.

Publications

Versican promotes T helper 17

Gain a holistic cytotoxic inflammation and impedes
understanding of gene oligodendrocyte precursor cell
remyelination
and protein expression Ghorbani S, et al. Nature Communications 2022.

in the tissue
microenvironment
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See how researchers are using spatial transcriptomics to

elevate the understanding of complex transcriptional
landscapes within a spatial context, which is essential for the Single-cell and spatial analysis reveal
understanding of biology and complex disease. interaction of FAP+ fibroblasts and
SPP1+ macrophages in colorectal
cancer
Qi J, et al. Nature Communications 2022.

Spatial transcriptomics of dorsal root

ganglia identifies molecular
signatures of human nociceptors
Tavares-Ferreira D, et al. Science Translational Medicine
2022.

View all Visium Spatial publications

Explore data The data generated by spatial capture technology allows you to choose any
gene of interest and display its spatially resolved expression on the original

visualization tissue section. Since the whole transcriptome is measured, you are not
limited to visualizing only a single gene. You can choose any number of
genes in any combination to view and analyze together.

Play with the data visualization and table below

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Visualization Controls Spatial Image t-SNE

Use the sliders under the tissue image Opacity

to adjust how you visualize and

combine the tissue image and the +
gene expression data. Colors −
represent clusters identified by
differentially expressed genes.

Leaflet

Cluster 1 2 3 4 5 6 7 8 9
Gene Identification
Nptxr 3.5 1.1 2.2 4.7 1.8 4.1 1.6 1.2 3.1
By placing the pointer above a gene Agt 0.59 2.0 3.6 1.2 0.78 0.42 3.2 2.6 0.61
name within the table, spots in the Ttr 3.5 4.9 3.0 4.8 3.1 2.6 2.7 2.8 3.8
tissue image will be colored based on
Pmch 0.77 1.8 4.5 1.5 0.56 0.79 1.3 0.63 0.66
the expression of that gene.
Camk2n1 5.7 3.7 3.9 5.8 3.9 6.8 4.3 4.2 5.1
Alternatively, by placing the pointer
above a value within the table, you Olfm1 5.6 2.8 3.5 5.9 3.1 5.5 3.2 3.6 4.5

can observe the expression of a Pcp4 4.9 2.8 4.2 4.4 2.0 2.5 3.3 6.2 3.0
specific gene with the spots from an Prkcd 0.50 0.81 0.72 0.51 0.48 0.31 1.6 4.7 0.43
individual cluster highlighted. Cck 5.5 2.4 2.3 4.8 3.0 5.2 2.3 4.4 4.2
Nnat 2.2 2.7 5.2 3.8 1.6 1.2 3.0 1.8 2.4

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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.
https://www.10xgenomics.com/spatial-transcriptomics
Spatial Transcriptomics - 10x Genomics
Turnkey solution
Compatible with diverse sample
types across preparation (FFPE
and fresh frozen) and species
(human, mouse, rat, and more),
easily incorporate into your
research with all the reagents
kitted and ready to use and no
specialized instrumentation
required.
Now available for order
View Spatial Products
ABOUT
Products
Easily adoptable workflow
Integrate easily with your current
laboratory methods and tools for
tissue analysis. Combine with
immunofluorescence staining and
imaging to gain multiomic
characterization in the spatial
context.
View Pricing
LEGAL NOTICES RESOURCES
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Streamlined data analysis
Analyze and understand gene and
protein expression heterogeneity
with Space Ranger analysis
software to process your data, and
interactively explore the results
with Loupe Browser visualization
software.
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