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GeoMx Human Whole Transcriptome Atlas (WTA)

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

GeoMx Human Whole Transcriptome Atlas (WTA)

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

  • 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.

  • 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.

  • 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:

  • Stem Cell Prolifiration

  • Cell Cycle

  • Senescence/Quiescence

  • Autophagy

  • Apoptosis

  • Anti-Apoptosis

  • PSC Pluripotency Markers and Regulators

  • Naive State/Primed State

Regulatory Pathways:​

  • Wnt/B-catenin Pathway

  • Hedgehog Signaling

  • AP-1 Signaling

  • PI3K-AKTmTOR Pathway

  • MAPK Pathway

  • JAK/STAT Pathway

  • Notch Signaling

Epigenetic Mechanism:

  • DNA Methylation

  • Histone Acetylation & Methylation

Mechano-Signaling:

  • Rho/ROCK Signaling

  • integrin/Cadherin Signaling

  • Hippo Pathway

Metabolism:

  • Oxidative Stress Response

  • Hypoxia Response

  • Amino Acid Metabolism

  • Fatty Acid Metabolism

  • Glutamine Metabolism

  • Glucose Metabolism

Differentiation Signaling and Pathways:

  • TGFB Signaling

  • Cytoskeletal Reorganization

  • MET/EMT Signaling

  • HOX Gene Activation

Differentiation Lineage:

  • Endodermal /Ectodermal /Mesodermal Lineage Markers

  • 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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