nCounter® Metabolic Pathways Panel


The NanoString nCounter Metabolic Pathways Panel allows for a reliable, simple, and robust way to quantify the expression of hundreds of genes involved in core metabolic processes and immunometabolism. The underlying molecular mechanisms behind alterations in metabolic pathways, signaling pathways, and cell stress can now be fully elucidated, giving researchers a complementary tool to traditional metabolite assays for profiling metabolic checkpoints and potential therapeutic targets.

Profile 768 genes in human or mouse across 34 annotated pathways involved in five important themes for metabolism research:

  • IM_MK1476_MetaPathwayPanel_FINAL_300x300.pngBiosynthesis and Anabolic Pathways
  • Nutrient Capture and Catabolic Pathways
  • Cell Stress
  • Metabolic Signaling
  • Transcriptional Regulation

Understand mechanisms of metabolic adaptation, metabolic switching and metabolic alterations, study changes in mitochondrial respiration and glycolysis, and advance efforts towards novel therapeutic targets.

  • Quantify the presence and relative abundance of 14 different immune cell types for immunometabolism studies
  • Bypass RT and amplification by direct detection, yielding highly reproducible data
  • Process your samples with < 30 minutes hands-on time and get results in < 24 hours

Receive publication-ready figures with off-the-shelf data analysis from nSolver.

Theme Description Pathways Number of Human Genes Number of Mouse Genes
Biosynthesis and Anabolic Pathways The processes involved in the production of complex macromolecules by enzyme-catalyzed biosynthetic pathways. The products of these pathways are required for nearly all cellular functions, including proliferation. Amino Acid Synthesis, Arginine Metabolism, Cell Cycle, Fatty Acid Synthesis, Glutamine Metabolism, Glycolysis, IDH1/2 Activity, Mitochondrial Respiration, Nucleotide Synthesis, Pentose Phosphate Pathway, Tryptophan/Kynurenine Metabolism, Vitamin and Cofactor Metabolism 354 348
Cell Stress Cells are impacted by the availability of nutrients and presence of toxic compounds. Adaptive responses to the stress are required for tumorigenesis, metastasis, and immune responses. DNA Damage Repair, Hypoxia, KEAP1/NRF2 Pathway, Reactive Oxygen Response 82 82
Nutrient Capture and Catabolic Pathways The processes involved in the breakdown of macromolecules, scavenging of cellular materials, or import of nutrients in order to stimulate ATP production or fuel anabolic pathways. Amino Acid Transporters, Autophagy, Endocytosis, Fatty Acid Oxidation, Glucose Transport, Lysosomal Degradation, Nucleotide Salvage 161 159
Metabolic Signaling The pathways that are commonly disrupted in cancer cells or altered in immune cells that impact metabolic function. In the context of cancer, mutations allow these regulated signaling pathways to allow for metabolic change enabling tumorigenesis. AMPK, mTOR, MAPK, Myc, NF-kB, p53 Pathway, PI3K, TCR and Costimulatory Signaling, TLR Signaling 237 235
Transcriptional Regulation Processes involved in the alteration of epigenetic and transcriptional activity of the cell that enables sustained metabolic reprogramming. This reprogramming allows for tumorigenesis and underlies stable changes in immune cell phenotype. Epigenetic Regulation, Transcriptional Regulation 77 69


Annotation Number of Human Genes Number of Mouse Genes
AMPK 48 48
Amino Acid Synthesis 93 89
Amino Acid Transporters 9 9
Arginine Metabolism 16 16
Autophagy 54 54
Cell Cycle 65 65
DNA Damage Repair 31 31
Endocytosis 39 41
Epigenetic Regulation 26 26
Fatty Acid Oxidation 24 21
Fatty Acid Synthesis 11 11
Glucose Transport 6 5
Glutamine Metabolism 31 30
Glycolysis 40 37
Hypoxia 15 15
IDH1/2 Activity 15 15
KEAP1/NRF2 Pathway 5 5
Lysosomal Degradation 16 16
mTOR 57 57
MAPK 52 52
Mitochondrial Respiration 73 72
Myc 20 20
NF-kB 27 27
Nucleotide Salvage 23 23
Nucleotide Synthesis 48 48
p53 Pathway 38 38
PI3K 82 82
Pentose Phosphate Pathway 19 19
Reactive Oxygen Response 37 37
TCR and Costimulatory Signaling 54 54
TLR Signaling 33 31
Transcriptional Regulation 59 51
Tryptophan/Kynurenine Metabolism 32 32
Vitamin and Cofactor Metabolism 28 28
Internal Reference 20 20


Cell Type Description Panel Genes
B Cells B cells are the primary mediators of the humoral immune response, bearing antigen-specific B cell receptors and producing antibodies that can enable the immune system to respond to a broad variety of antigens. B cells can also function as MHC class II antigen presenting cells to stimulate T cell immunity. BLK, CD19, CD20, TNFRSF17
T Cells T-cells mediate cell-based immunity by recognizing primarily peptide antigens displayed on MHC class I or class II and either producing cytokines or directly killing the presenting cell. CD3D, CD3E, CD3G, CD6, SH2D1A
TH1 CD4+ T cell subset that produces IL2 and Interferon-gamma to promote cellular immunity by acting on CD8+ T Cells, NK Cells and Macrophages. TBX21
Regulatory T Cells (Tregs) CD4+ T Cells that suppress effector B and T Cells and play a central role in suppression of the immune response and tolerance to self-antigens. FOXP3
CD8+ T Cells A subset of T cells that are capable of binding cognate-antigen expressing cells via class I MHC and directly lysing them via perforin and granzymes. CD8A, CD8B
Exhausted CD8+ T Cells T-cells overstimulated by antigen can develop an "exhausted" phenotype, in which they are no longer effective in targeting antigen-bearing cells. CD244, EOMES, CD223
Cytotoxic Cells All cells capable of cytotoxic activity, which can include T, NKT, and NK-cells. CTSW, GNLY, GZMA, GZMB, GZMH, CD161, CD94, KLRK1, PRF1
Dendritic Cells Professional antigen presenting cells that internalize, process, and present antigens to lymphocytes via MHC class I and class II along with costimulatory signals to initiate cellular immune responses. CCL13, CD209, HSD11B1
Macrophages Pluripotent cells with critical roles in initiating innate and adaptive immune responses, phagocytosing abnormal cells, and regulating wound healing and tissue repair. CD163, CD68, CD84
Mast Cells Mast cells release histamine containing granules and other signals in order to promote inflammation and regulate allergic responses. MS4A2, TPSAB1
Neutrophils Neutrophils are highly abundant cells that respond early to sites of infection or inflammation, phagocytose cellular debris, and promote downstream immunity. CSF3R, CD16, S100A12
Natural Killer (NK) Cells Cytotoxic cells of the innate immune system that are a significant source of interferon-gamma and are capable of directly killing targeted cells via detection of a loss in MHC surface expression. NKP46, XCL2
NK CD56dim cells The amount of CD56 present on an NK cell is indicative of its age and differentiation state; CD56 dim cells are mature NK cells, more commonly found in peripheral blood than secondary lymphoid tissues, and have the greatest cytolytic activity. IL21R, KIR2DL3, KIR3DL1, KIR3DL2


Feature Specifications
Number of Targets 768 (Human), 768 (Mouse), including internal reference genes
Sample Input - Standard (No amplification required) 25-300 ng
Sample Input - Low Input As little as 1 ng with nCounter Low Input Kit (sold separately)
Sample Type(s) Cultured cells/cell lysates, sorted cells, FFPE-derived RNA, total RNA, fragmented RNA, PBMCs, and whole blood/plasma
Customizable Add up to 30 unique genes with Panel-Plus and up to 10 custom protein targets
Time to Results Approximately 24 hours
Data Analysis nSolver™ Analysis Software (RUO)


Selected Panel References:

  1. Peng, X et al. Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell Reports. 2018;23(1):255-69.
  2. DeBerardinis RJ, Chandel, NS. Fundamentals of Cancer Metabolism. Science Advances. 2016;2(5).
  3. O’Neill LA et al. A Guide to Immunometabolism for Immunologists. Nature Reviews Immunology. 2016;16(9):553-65.
  4. Stine, ZE et al. MYC, Metabolism, and Cancer. Cancer Discovery. 2015;10:1024-39.
  5. Renner, K et al. Metabolic Hallmarks of Tumor and Immune Cells in the Tumor Microenvironment. Frontiers in Immunology. 2017;8:248.
  6. Andrejava, G and Rathmell, JC. Similarities and Distinctions of Cancer and Immune Metabolism in Inflammation and Tumors. Cell Metabolism. 2017;26(1):49-70.
Product Product Description Quantity Catalog Number
nCounter Human Metabolic Pathways Panel Includes 768 genes; 20 internal reference genes for data normalization 12 Reactions XT-CSO-HMP1-12
nCounter Mouse Metabolic Pathways Panel Includes 768 genes; 20 internal reference genes for data normalization 12 Reactions XT-CSO-MMP1-12
nCounter Master Kit (Max or FLEX Systems) Reagents and Cartridges Reagents, cartridges, and consumables necessary for sample processing on nCounter MAX and FLEX Systems 12 Reactions NAA-AKIT-012
nCounter SPRINT Cartridge 1 Cartridge, 12 lanes Sample Cartridge for nCounter SPRINT System 12 Reactions SPRINT-CAR-1.0
nCounter SPRINT Reagent Pack nCounter SPRINT Reagent Pack containing Reagents A, B, C, and Hybridization Buffer 192 Reactions SPRINT-REAG-KIT


For Research Use Only. Not for use in diagnostic procedures.