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GeoMx Human Whole Transcriptome Atlas (WTA)
Prosigna Score / ROR Score:
The ROR Score has been validated to predict the risk of recurrence of disease in ER+ breast cancer after surgery and treatment with 5 years of endocrine therapy. The ROR score depends upon the biology of the intrinsic subtypes, the proliferation score of the tumor, and the tumor size as shown in the equation below:
ROR = aRLumA + bRLumB + cRHer2 + dRBasal + eP + fT
Each of the R variables in the equation above indicate the Pearson correlation coefficient of the PAM50 expression profile for the tumor compared to each of the prototypical centroids for the intrinsic subtypes shown in the heatmap below. P is the proliferation score, which is the average gene expression profile of genes associated with cell-cycle progression and T is the tumor stage.
Figure: Heatmap of PAM50 genes by subtype. Red is higher expression and green is lower expression
Full Transcriptome Spatial RNA Analysis
The GeoMx Human Whole Transcriptome Atlas (GeoMxHu WTA) is designed for comprehensive profiling of spatial biology. With full coverage of protein coding genes, GeoMxHu WTA delivers spatial analysis of any target in any tissue in the biological regions that matter most.
The GeoMx Human Whole Transcriptome Atlas (GeoMxHu WTA) provides an unbiased view of 18,000+ protein-coding genes. The GeoMx Human WTA unlocks new pathways to be explored by researchers and enables GeoMxRNA profiling in oncology, immunology, neuroscience, developmental biology, and other diverse fields. GeoMx Hu WTA provides robust and sensitive performance on FFPE or Fresh Frozen samples.
GeoMx DSP COVID-19 Protein and RNA Analysis
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Rapidly perform high-plex spatial analyses of the host response in FFPE or fresh frozen tissue using the GeoMx Digital Spatial Profiler (DSP). NanoString’s GeoMx DSP platform enables high-plex protein and RNA experiments in key areas of biology such as molecular response, cellular (immune) response, tissue damage, and drivers of individual susceptibility to severe forms of disease.
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The GeoMx COVID-19 Immune Response Atlas, a ~1,850-plex RNA assay, enables spatial studies of the SARS-CoV-2 virus and host response. RNA targets include COVID-19 receptors and proteases, pulmonary alveolar type I and II markers, lung biology markers, viral response markers, and SARS-CoV-2 probes. RNA targets are profiled simultaneously using the GeoMx DSP and an Illumina next-generation sequencer (NGS) for readout. Users can run ACD RNAscope™ probes alongside GeoMx RNA probes to identify regions of interest.
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A five-antibody custom, ready-to-go protein panel, with receptor, protease, and viral markers is available through the GeoMx Technology Access Program or for order through Abcam. This COVID-19 GeoMx-formatted Antibody is run with the 20-plex GeoMx Immune Cell Profiling Core (plus controls) with readout on the nCounter Analysis System. Users can add up to six 10-plex modules including the Immune Activation Status, Immune Cell Typing, and/or Cell Death modules to more deeply profile proteins involved in T cell activation and cell death. NanoString scientists can recommend commercially-available markers for lung epithelium, nasal epithelium, immune response markers, and the viral spike protein.
High Sensitivity
Superior sensitivity to detect 1000s of unique human genes in <50 µm regions
Comprehensive Coverage
Whole transcriptome coverage with probes specific to protein coding mRNA sequences
Robust Performance
Robust performance across sample types including FFPE with high concordance with RNA-seq and RNAscope™
Customizable
Flexibility to customize with up to 60 additional targets to assay non-coding RNA, synthetic DNA or exogenous genes
Discover a new way to look at biology
The eight essential components of stem cell biology
Stemness
Pluripotency
Regulatory Signaling
Epigenetics
Mechano-Signaling
Metabolism
Differentiation Signaling
Lineage Specification
Stem Cell Renewal:
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Stem Cell Prolifiration
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Cell Cycle
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Senescence/Quiescence
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Autophagy
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Apoptosis
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Anti-Apoptosis
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PSC Pluripotency Markers and Regulators
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Naive State/Primed State
Regulatory Pathways:
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Wnt/B-catenin Pathway
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Hedgehog Signaling
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AP-1 Signaling
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PI3K-AKTmTOR Pathway
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MAPK Pathway
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JAK/STAT Pathway
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Notch Signaling
Epigenetic Mechanism:
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DNA Methylation
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Histone Acetylation & Methylation
Mechano-Signaling:
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Rho/ROCK Signaling
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integrin/Cadherin Signaling
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Hippo Pathway
Metabolism:
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Oxidative Stress Response
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Hypoxia Response
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Amino Acid Metabolism
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Fatty Acid Metabolism
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Glutamine Metabolism
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Glucose Metabolism
Differentiation Signaling and Pathways:
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TGFB Signaling
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Cytoskeletal Reorganization
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MET/EMT Signaling
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HOX Gene Activation
Differentiation Lineage:
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Endodermal /Ectodermal /Mesodermal Lineage Markers
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Key Somatic Cell Types
Custom & Clinical Products
Assay Type
Product
Maximum Targets
Daily Sample Throughput
Analytes Offered
Common Applications
Custom codeSets
Elements TagSets
PlexSet Reagents
Self-assembled, interchangeable probes, optimized for smaller validation projects with maximum flexibility
Self-assembled, interchangeable probes for high-throughput, sample multiplexing projects
User-designed, turn-key solution that comes ready-to-use
216
96
800
24-96
24-96
192-1152
mRNA, CNV, Fusions
mRNA, Fusions
mRNA, miRNA, CNV, Fusions
Cell line drug screen, biomarker development, infectious disease
Gene Signature Development
Model Organism, Microbes, Agriculture
GeoMx Mouse Whole Transcriptome Atlas Mouse RNA for Illumina Systems RNA Probe set that targets 21,000+ transcripts for mouse protein coding genes plus ERCC negative controls to profile the whole transcriptome. Excludes uniformative high expressing targets such as ribosomal subunits. Includes RNA probes designed for Illumina NGS readout with the Seq Code library prep.
Description
4 Slides
Pack Size
GMX-RNA-NGSMsWTA-4
SKU
GeoMx Human Whole Transcriptome Atlas Human RNA for Illumina Systems RNA Probe set that targets 18,000+ transcripts for human protein coding genes plus ERCC negative controls to profile the whole transcriptome. Excludes uninformative high expressing targets such as ribosomal subunits. Includes RNA probes designed for Illumina NGS readout with the Seq Code library prep.
Description
4 Slides
Pack Size
GMX-RNA-NGSHuWTA-4
SKU
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 Pan-CK, CD45, and a nuclear stain.
Description
12 slides
Pack Size
GMX-RNA-MORPHHST-12
SKU
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.
Description
12 slides
Pack Size
GMX-RNA-MORPHHMEL-12
SKU
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.
Description
192 AOI
Pack Size
GMX-NGS-SEQ-[XX]
SKU
GeoMx RNA Slide Prep Kit for FFPE Sample prep reagents for GeoMx DSP RNA analysis. Includes Buffer W, Buffer S, and Buffer R.
Description
12 slides
Pack Size
GMX-PREP-RNAFFPE-12
SKU
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.
Description
1 Pack
Pack Size
GMX-DSP-COLL-PLT
SKU
GeoMx DSP Instrument 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.
Description
1 Kit
Pack Size
GMX-DSP-BUFF-KIT
SKU
GeoMx DSP Instrument 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
Description
1 Kit
Pack Size
GMX-DSP-BUFF-KIT
SKU
SKU
Description
Pack Size
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AUTOIMMUNE DISEASE AND CHRONIC INFLAMMATORY DISEASE COVERAGE
Condition
Description
Chronic inflammatory disorder that impacts the lining of joints.
Chronic inflammatory of the digestive tract.
Autoimmune disease is where the immune system mistakenly attacks the insulin-producing cells of the pancreas
Demyelinating disease that disrupts communication with the nervous system.
Immune-mediated disease that causes skin cells to rapidly build up on the surface of the skin
Certain treatments and infections have been reported to interfere with the immune system and induce a series of autoimmune disease or adverse immune-related events.
Chronic inflammatory disease that manifests systematically throughout the body.
Rheumatoid Arthritis
Inflammatory Bowel Disease
Type 1 Diab
Type 1 Diabetes
Multiple Sclerosis
Systematic Lupus Erythematosus
Psoriasis
Induced Adverse Immune Events
Immune Checkpoint Coverage
ADORA2A(A2aR)
CD70
HAVCR2(TIM3)
CD274(PD-L1)
TNFRSF9(4-1BB)
TNFSF9(4-1BBL)
TNFRSF18(GITR)
TNFSF18(GITRL)
VSIR(VISTA)
PDCD1LG2(PD-L2)
TIGIT
TNFRSF4(OX40)
TNFSF4(OX40L)
ICOS
ICOSLG(B7-H2)
LAG3
PDCD1(PD-1)
CD80
CD86
CD276(B7-H3)
CTLA-4
CD27
CD28
CD40
CD40LG
Functional Annotations
Pathways Regulating Glia
(178/180 Hs/Mm Genes)
Inflammation & Peripheral Immune Invasion
(187/188 Hs/Mm Genes)
Cell Stress & Damage Response
(127/134 Hs/Mm Genes)
Angiogenesis
Apoptosis
Autophagy
Cell Cycle
Hypoxia
NO Metabolism and Signaling
Oxidative & Nitrosative Stress
Proteotoxic Stress
Calcium Signaling
Circadian Signaling
Ion Transport
JAK-STAT
Lipid Metabolism
MAPK & PI3K
TGF-Beta Signaling
Wnt Signaling
Antigen Processing & Presentation
Cell Migration
Chemokines
Complement System
Cytokines
Inflammasome
Interferon Signaling
NK-kappaB Signaling
Phagocytosis
T-Cell Signaling