Trekker™ Single-Cell Spatial Mapping Kit PDF Free Download
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Product note Trekker™ Single-Cell Spatial Mapping Kit
Discover more at takarabio.com/Trekker-resources
Delivering true single-cell spatial omics
While single-cell genomics has greatly advanced our understanding of how cells function in tissues and organs,
the missing component is where cells are organized in their natural spatial context.
The Trekker Single-Cell Spatial Mapping Kit elevates single-cell research by transforming standard single-cell
genomics data into spatial data. Trekker technology works by tagging each nucleus within its native tissue environment
with unique spatial barcodes. These spatial barcodes are read using next-generation sequencing (NGS), allowing
each nucleus to be bioinformatically positioned in its spatial coordinates. The result is a spatial map with true
single-cell resolution, without the use of complex instrumentation, cell-type deconvolution, or cell segmentation.
Designed as a simple reagent kit, Trekker spatial mapping integrates seamlessly with existing single-cell sequencing
workflows and preserves the high molecular sensitivity of single-cell data. Moreover, Trekker technology extends
beyond spatial transcriptomics to other omics assays, broadening the scope of spatial analysis.
True single-cell spatial resolution
Single-cell resolution every time —no deconvolution,
no segmentation, no complex algorithms
UMAP to spatial map
One-of-a-kind spatial solution designed specifically for single-
cell data
Versatility
Fits into any single-cell sequencing workflow
Simplicity
Simple 1-hour workflow with no specialized instrumentation
Beyond spatial transcriptome
Venture into spatial single-cell multi-ome analysis
Same single-cell data
Preserve the quality and sensitivity of single-cell data
Trekker Single-Cell Spatial Mapping Kit
Product note
takarabio.comTrekker Single-Cell Spatial Mapping Kit product note 2
Oligodendrocytes
Hippocampus
CA1
CA2/3
DG
Medial habenula
Cortical layers
L2-3 IT
L4
L5 IT
L5 PT
L6 CT
L6 IT
L6b
Thalamus, hypothalamus,
striatum
Hypothalamus 1
Hypothalamus 2
Striatum 1
Striatum 2
Striatum 3
Thalamic Pvalb+
Thalamic nucleus
CA2/3
DG
Ependymal 1
Ependymal 2
Pvalb+
Lamp5+
Sncg+
Sst+
Medial habenula
V3 1
V3 2
Striatum 1
Striatum 2
Striatum 3
Thalamic nucleus
Thalamic Pvalb+
Hypothalamus 1
Hypothalamus 2
Unassigned
Macrophage/microglia
Oligodendrocyte
Polydendrocyte
Astrocyte 1
Astrocyte 2
Endothelial
SMC
Pericyte
L2-3 IT
L4
L5 IT
L5 PT
L6 CT
L6 IT
L6b
NP
Retrosplenial
CA1
Lpl
Otof
Wfs1
Arhgap6
Igsf11
Rspo1
Tspan11
Rorb
Adam33
Cbln4
Fam107a
Deptor
Sdc4
Kcnj10
Acsbg1
Lratd2
Bcl6
Tcerg1l
Tr mt9b
Parm1
Syt6
Foxp2
Ighm
Rprm
Oprk1
Gnb4
Nr4a2
Rgs12
Synpr
Ccn2
Nxph4
Cplx3
Moxd1
Cacng5
Sncaip
Cxcl14
Htr2c
Sv2c
Tshz2
L2−3 IT
L4
L5 IT
L5 PT
L6 CT
L6 IT
L6b
RSPv
ln (CPM+1)
0
2
4
6
Percent
Expressed
0
25
50
75
A
C
B
D
Spatial mapping of nuclei from an adult mouse brain. 27,275 nuclei from a 25 µm tissue section of an adult mouse brain were spatially
positioned using a 10 mm x 10 mm Trekker tile. Each dot in the UMAP (Panel A) represents a single nucleus, with a 1:1 correspondence
to the spatial map (Panel B), where dots are color-coded by gene expression patterns from snRNA-seq data. The top differentially
expressed genes for each cortical layer, as measured by snRNA-seq, are shown (Panel C). Specific features of the brain section and
known cell types are highlighted (Panel D).
Trekker Single-Cell Spatial Mapping Kit
Product note
takarabio.comTrekker Single-Cell Spatial Mapping Kit product note 3
Generate high-density nuclei spatial map while preserving single-cell data quality
Seamless integration with single-cell sequencing workfl ow
Spatial mapping of nuclei from an embryonic day 11 (E11) mouse embryo using the Trekker workfl ow. 57,545 nuclei from a 25 µm
tissue section of an E11 mouse embryo were spatially positioned using a 10 mm x 10 mm Trekker tile. Panel A. Spatial map of the
positioned nuclei. Each dot represents a single nucleus. Panel B. H&E-stained image of an adjacent tissue section demonstrates high
concordance, underscoring the accuracy of spatial feature preservation by the Trekker kit. Panel C. Trekker spatial data aligned with
the adjacent H&E image using STalign. Panel D. UMAP with 1:1 correspondence to each dot in the spatial map. Nuclei are color-coded
based on gene expression patterns derived from snRNA-seq data. Panel E. Spatial expression patterns of Gm3764, Rtn1, Cpox, Ddm3os,
and Gata3 overlaid with the H&E image in Panel B.
Adjacent H&ETrekker map
Liver
Heart
Jaw & tooth
Mucosal
epitheliu
m
Muscle
Brain
Spinal
cord
Dorsal root
ganglion
Rib
Lung
Stomach
GI tract
UMAP1
UMAP2
A B Trekker map
overlaid on H&E
CUMAP
D
Gm3764 Rtn1 Cpox Dnm3os Gata3
E
The core of the Trekker technology lies in its spatially barcoded surface, composed of a bead monolayer. A 25 µm frozen
tissue section is placed onto this barcoded substrate. Upon exposure to UV light, oligonucleotides carrying spatial barcodes are cleaved
from the beads and attach to the nuclei in their vicinity. The tissue is then dissociated from the substrate, and the nuclei are isolated.
Single-nucleus RNA sequencing (snRNA-seq) is performed on these isolated nuclei containing spatial barcode oligos. Spatial barcode
oligos are captured and amplifi ed alongside cellular RNA. For each sample, two sequencing libraries are generated—one for gene
expression data and another for spatial barcodes. A custom bioinformatics pipeline is used to map the position of each nucleus based
on the spatial barcodes it contains. Integrating the Trekker protocol adds just one hour upstream of standard snRNA-seq workfl ows.
Handshake
sequence
Spatial barcode
Photo-cleavable
Linker
UV
Bead with
spatial barcode
Melt tissue
on Trekker tile
Tag nuclei with
photocleaved
spatial barcode
Isolate
nuclei
Single nucleus
RNA-seq
Trekker bioinformatics
analysis places nuclei
in space based on spatial
barcodes associated
with each nucleus
Trekker Single-Cell Spatial Mapping Kit
Product note
Takara Bio USA, Inc.
United States/Canada: +1.800.662.2566 • Asia Pacific: +1.650.919.7300 • Europe: +33.(0)1.3904.6880 • Japan: +81.(0)77.565.6999
For Research Use Only. Not for use in diagnostic procedures.
© 2025 Takara Bio Inc. All Rights Reserved. All trademarks are the property of Takara Bio Inc. or its affiliate(s) in the U.S. and/or other countries or their respective owners.
Certain trademarks may not be registered in all jurisdictions. Additional product, intellectual property, and restricted use information is available at takarabio.com. 4.25 US (634092)
Product features
Spatial resolution True single-cell
Sample type Fresh frozen tissues
Tile size 10 mm x 10 mm
Specialized capital equipment None required
Required auxiliary equipment Cryostat, single-cell sequencing platform, next-generation sequencer
Workflow duration 1 hr upstream of single-cell workflow
Sensitivity Same as the molecule capture sensitivity of the single-cell workflow of choice
Single-cell workflow compatibility
Supported
• 10x Chromium Single Cell 3' RNA v3.1, v4
• BD Rhapsody WTA
User-demonstrated protocols
• BD Rhapsody Single-Cell ATAC-Seq and mRNA WTA
• BD Rhapsody Single-Cell TCR/BCR Next and mRNA WTA
PRODUCTS
Cat. # Product
SK017 Trekker U 10x10 Bundle (4 Tiles)
K 011 Trekker Starter Kit (UV Lamp and Accessories)
SK020 Trekker 10x10 Training Kit Bundle (2 Tiles)
Discover more at takarabio.com/Trekker-resources
