PRODUCT BULLETIN

GeoMx® Cancer Transcriptome Atlas
Profile over 1,800 RNA targets simultaneously with spatial resolution in any region of interest from a single tissue section using theGeoMx Digital Spatial Profiler (DSP). The GeoMx Cancer Transcriptome Atlas (CTA) is designed for comprehensive profiling of the tumor,
tumor microenvironment, and tumor immune status.

Product Highlights•

Comprehensive RNA content designed for cancer
biology research•

Expansive coverage of the immune response,
tumor microenvironment, and tumor biology•

Includes clinically relevant gene sets from BC 360
and IO 360 such as the Tumor Inflammation Signatureand PAM50•

Over 100 pathways to explore all aspects of cancer•Compatible with RNAscope™ andantibody morphology markers•

Supplement with up to 60 additional targets of interest•

For use with Illumina next-generation sequencer (NGS)
readout•

Utilize the GeoMx Data Center for interactive analysis

GeoMx® Cancer Transcriptome Atlas Design
Designed to profile over 1,800 RNA targets simultaneously with spatial resolution, the Cancer Transcriptome Atlas (CTA) contains targets for broadcell profiling and includes necessary controls for all GeoMx DSP experiments. The CTA covers 112 pathways critical to immune response, tumor biology,
and the microenvironment. GeoMx RNA assays contain in situ hybridization (ISH) probes conjugated to unique DNA indexing-oligonucleotides via aUV-photocleavable linker. After selecting regions of interest (ROI) on GeoMx DSP, the DNA oligonucleotides are UV cleaved and then sequenced onan Illumina sequencer. DNA oligonucleotide sequences contain ROI indices mapping them back to their tissue location, an RNA target identification
sequence matching them to their ISH probes, and a unique molecular identifier (UMI) to deduplicate reads. Sequenced oligonucleotides areprocessed, then imported back into the GeoMx Data Center platform for integration with the slide images and ROI selections for spatially-resolved
RNA expression.

FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.

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GeoMx® Cancer Transcriptome Atlas

PRODUCT BULLETIN

Curated Content for Cancer Biology

Validated Assays Ready for Use

The GeoMx CTA is designed to profile all aspects of tumor andtumor microenvironment biology. Accompanying Morphology
Marker Kits are available for tissue visualization and ROI
selection.

All GeoMx RNA assays undergo extensive validation to ensurehigh quality GeoMx DSP data.

Adaptive Immunity
T cells B cells
TCR & BCR Signaling
Cancer Antigens
MHC Class I & II Antigen Presentation
T-cell Checkpoints
TH1, TH2, TH9, Th17, and Treg Differentiation

Immune Response
Chemokine Signaling
Cytotoxicity
IL-1, IL-2, IL-6 & IL-17 Signaling
Immune Exhaustion
Interferon Response Genes
Lymphocyte Regulation & Trafficking
NF-kB Signaling
Other Interleukin Signaling
Prostaglandin Inflammation
TNF Signaling
Type I, II, & III Interferon Signaling

Cell Function
Apoptosis
Autophagy
Cell Adhesion & Motility
Cell Cycle
Cilium Assembly
Differentiation
DNA Damage Repair
EMTEndocytosis
Epigenetic Modification
Immortality & Stemness
Ion Transport
Lysosome
Oxidative Stress
Phagocytosis
Proteotoxic Stress
RNA Processing
SenescenceMetabolism
Amino Acid Synthesis & Transport
Arginine & Glutamine Metabolism
Fatty Acid Oxidation & Synthesis
Glycolysis & Glucose Transport
Glycosylation
IDH1/2
Lipid Metabolism
Mitochondrial Metabolism / TCA
Nucleotide Synthesis
Pentose Phosphate
Tryptophan & Kynurenine Metabolism
Vitamin & Cofactor Metabolism

Tissue Compartment
Tumor Biology
Immune Response
Microenvironment#GenesInnate Immunity#Genes130
194
188627107

Complement System
Dendritic Cells
DNA & RNA Sensing
Glycan Sensing
Host Defense Peptides
Inflammasomes
Myeloid Inflammation
Neutrophil Degranulation
NK Activity
NLR Signaling
RAGE Signaling
TLR Signaling

49
19107
63
22
1196
124
94
88
8135

Signaling Pathways#Genes#Genes
121
6168
2025
202
114
173
496
103

#Genes
121
62
139
167
10225
90
98
57
166
33
37
14151
105
2235
128

#Genes55
51
1529
12107852107428#Genes1454
1481
978AMPK Signaling
Androgen Signaling
EGFR Signaling
ERBB2 Signaling
Estrogen Signaling
FGFR Signaling
FoxO Signaling
GPCR Signaling
Hedgehog Signaling
HIF1 Signaling
Insulin Signaling

44321721844079177456881

JAK-STAT Signaling

118

MAPK Signaling

261

MET SignalingmTOR Signaling
MycNO Signaling
Notch Signaling
p53 Signaling
PDGF Signaling
PI3K-Akt Signaling
PPAR Signaling
Purinergic Signaling
Retinoic Acid Signaling
TGF-beta Signaling
VEGF Signaling
Wnt Signaling

3476
261074763024215356969124

Physiology & DiseaseAngiotensin System
Circadian Clock
Drug Resistance
Glioma
Leukemia
Matrix Remodeling andMetastasis
Melanoma
Neuroendocrine Function
Prostate Cancer

Tissue Compartment
Tumor
ImmuneStromaFOR RESEARCH USE ONLY. Not for use in diagnostic procedures.

Bioinformatics
DesignSensitivity/Specificity
Testing

Sequences screened
for specificity andcross hybridization

Quantitative assessment
on control FFPE
cell pellets

TissueStudies

Pooling
ScreenAnalysis of normal andtumor tissue microarrays toconfirm performance in tissue

Probe pools aretested for equimolar
concentrations

Spatial RNA Profilingwith High Reproducibility
RNA detection shows high reproducibility between regionsof interest selected from 6 cell lines within a cell pellet array(FIGURE 1).

#Genes52236093

Variability between ROIs

5270892

R² = 0.96#Genes
1622
1396
1024

Figure 1 : High reproducibility between two 300 μm ROIs selected in 6
different cell lines. An example cell pellet is pictured above with ROIs
selected.
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NanoString Technologies, Inc.

GeoMx® Cancer Transcriptome Atlas

High Sensitivity Across All Targets

Reveal Tissue Heterogeneity

The GeoMx CTA detects high, medium, and low expressing genes withbroad coverage of the genes in The Cancer Genome Atlas (TCGA)².

Segmentation analysis of a region of interest (ROI) from a non-small
cell lung cancer (NSCLC) sample demonstrates distinct RNA expression
profiles in the tumor and tumor microenvironment segments, which
would be lost if profiling the ROI as a whole (FIGURE 3).

Detection of low, medium,and high expressors in single
region of interest in non-small
cell lung cancer sample

Expression in
one wholeregionExpression in
one tumorregion

Expression inone TME
region1800+ genesFigure 2: Coverage of the CTA compared to the TCGA with equally-sizedbins of low, medium, and high expressors based on TCGA expression
level data (left). Average TCGA expression levels below 1 FPKM are
categorized as not detected.

Figure 3: ROIs were selected with mixed tumor and tumor microenvironment(immune) segments in NSCLC tissue. ROIs were segmented based on PanCKand SYTO 13 (nuclear) morphology stain. RNA expression demonstrates distinct
profiles in the tumor as compared to the microenvironment segments.

Comprehensive Coverage for Cancer Biology
Designed for cancer biology research, the Cancer Transcriptome Atlas provides complete coverage of tumor biology, the microenvironment,
and the immune response, without sequencing unnecessary targets.

Figure 4: Cancer Transcriptome Atlas Pathways Analysis (left) compared to the Whole Transcriptome Pathways Analysis (right) illustrates the comprehensive coverage of
the Cancer Transcriptome Atlas, which encompasses all areas of biology including signal transduction, metabolism, and the immune system³. Increasing the number of RNA
targets from the 1,800+ CTA targets to the whole transcriptome yields only a minimal increase in coverage of cancer biology.

FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.

3PRODUCT BULLETIN

GeoMx® Cancer Transcriptome Atlas

GeoMx® Data Center
Unique GeoMx Data Center software uniquely combines whole tissue visualization at single cell resolution with advanced ROI selection toenable comprehensive spatial profiling of tissue sections. The fully integrated workflow tracks image data to corresponding profiling data,
allowing users to easily go from data collection to data analysis and to interact with either dataset in real time. The data analysis moduleassesses the quality of the raw data and provides a number of options to normalize data sets. Moreover, a variety of data visualization
formats are enabled to export publication-quality figures. Visualization plots include: heatmap, cluster, bar graph, box plot, scatter plot,line/trend plot, strip plot, volcano plot, and PCA.
To view the RNA probe list visit: nanostring.com/geomxassays

Ordering Information
GeoMx Cancer Transcriptome Atlas
ProductProduct Description

Quantity

Catalog Number

GeoMx Cancer Transcriptome Atlas
Human RNA for Illumina Systems

RNA panel including over 1,800 targets plus controls for humanimmune response, tumor biology, and microenvironment.
Includes RNA probes for Illumina NGS readout.

4 slides

GMX-RNA-NGS-CTA-4

Quantity

Catalog Number

GeoMx Morphology Kits
ProductProduct Description

GeoMx Solid Tumor TME
Morphology Kit
Human RNA Compatible

Morphology kit for visualization of human solid tumors
and the tumor microenvironment. For use with RNA
assays. Includes fluorescent antibodies against PanCK,CD45, and a nuclear stain.

12 slides

GMX-RNA-MORPH-HST-12

GeoMx Melanoma TME
Morphology Kit
Human RNA Compatible

Morphology kit for visualization of human melanoma
and the tumor microenvironment. For use with RNA assays.
Includes fluorescent antibodies against S100B/Pmel17,
CD45, and a nuclear stain.

12 slides

GMX-RNA-MORPH-HMEL-12

Additional Assay Reagents
ProductProduct Description

Quantity

Catalog Number

GeoMx Seq Code Pack
Compatible with Illumina Systems

NGS readout reagents for GeoMx DSP RNA and protein
analysis. Includes two Seq Code primer plates (choice of A&B,C&D, E&F, or G&H) and two universal enzyme master mixes.

192 AOI

GMX-NGS-SEQ-[XX]GeoMx RNA Slide
Prep Kit for FFPESample prep reagents for GeoMx DSP RNA analysis. Includes
Buffer W, Buffer S, and Buffer R.

12 slides

GMX-PREP-RNA-FFPE-12

GeoMx DSP Collection Plate

Barcoded collection plates for use on the GeoMx DSP.
Required for AOI tracking. Kit includes 12 plates
covering 1,152 AOI.

1 PackGMX-DSP-COLL-PLT-4

GeoMx DSP Instrument
Buffer Kit

Buffer kit for the GeoMx DSP. Includes Buffer S and Buffer
H. Sufficient for ~48 samples with ~18 AOI each. Volume
requirements may vary based on experimental design.

1 Kit

GMX-DSP-BUFF-KITReferences
1.
2.
3.

Ayers, Mark, et al. IFN-γ–related mRNA profile predicts clinical response to PD-1 blockade. Journal of Clinical Investigation. 127.8 (2017).
National Cancer Institute: The Cancer Genome Atlas Program. cancer.gov/tcga
Pathway Analysis figures from Reactome, Copyright 2020 Reactome, License CC BY 4.0. Image cropped from original.

For more information, please visit nanostring.com/GeoMxDSP
NanoString Technologies, Inc.
T (888) 358-6266
530 Fairview Avenue NorthF (206) 378-6288
Seattle, Washington 98109

nanostring.com
info@nanostring.com

Sales Contacts
United States us.sales@nanostring.com
EMEA: europe.sales@nanostring.com

FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
© 2017-2021 NanoString Technologies, Inc. All rights reserved. NanoString, NanoString Technologies, GeoMx are registered trademarks of NanoString
Technologies, Inc., in the United States and/or other countries.
AUG 2021 MK2229

Asia Pacific & Japan apac.sales@nanostring.com
Other Regions info@nanostring.com