nCounter® Neuroinflammation Panels

Perform comprehensive multiplex gene expression analysis in human or mouse with 770 genes included for research of immunity and inflammation, neurobiology and neuropathology, and metabolism and stress.

  • Neuro research areas: immunity and inflammation, neurobiology and neuropathology, and metabolism and stressFor research of neurodegenerative disease, traumatic brain injury, psychiatric disorders, neuropathic pain, CNS infection, and others
  • Comprehensive assessment of 23 neuroinflammation pathways and processes
  • Unique cell typing analysis feature measures the relative abundance of 19 CNS and peripheral immune cells
  • Customizable with Panel Plus option – add up to 55 genes of your choosing

Download gene lists:

Learn about our nCounter Analysis System and nSolver™ Analysis Software.


Cell Press Selections

Read "Pathological Mechanisms of Neurodegeneration" in the Cell Press Supplement.

Cell Press Supplement Pathological Mechanisms of Neurodegeneration

Application Note

Read "Deciphering the Complexities of Neurodegeneration and Neuroinflammation" application note about gene expression.

Neuropathology Application Note

CNS and peripheral immune cell profiling

Genes included in the Neuroinflammation Panels provide unique cell profiling data for measuring the relative abundance of 19 CNS and peripheral immune cell types in a single sample1. The table below summarizes each cell type represented by gene content in the panel qualified through biostatistical approaches and selected literature in the field of neuroinflammation research.

CNS Cells

Cell Type Human Genes Mouse Genes
Neurons 6 6
Microglia 6 6
Astrocytes 8 8
Oligodendrocytes 15 15
Endothelial cells 9 9


Peripheral Immune Cells

Cell Type Human Genes Mouse Genes
B cells 7 7
Dendritic cells 2 2
Exhausted CD8 4 4
Macrophages 4 4
T cells 6 6
CD8 T cells 2 2
Neutrophils 5 3
Mast cells 4 4
Cytotoxic cells 9 8
Tregs 1 1
NK CD56dim cells 2 3
NK cells 2 2
CD45+ cells 1 1
Th1 cells 1 1


Danaher P. et al. Gene expression markers of Tumor Infiltrating Leukocytes JITC 2017


Functional annotations for 23 pathways and processes were assigned across the genes in the Neuroinflammation Panels. The 23 pathways and processes represent three core themes of neuroinflammation: immunity and inflammation, neurobiology and neuropathology, and metabolism and stress.

Immunity and Inflammation

The role of innate immunity in many neurological disorders is now widely accepted in the research world although the relative contributions of these processes to the progression and/or amelioration of these diseases is incompletely understood. Several key processes and pathways are assessed in this panel to provide a comprehensive view of the immune and inflammatory response in the nervous system.

Functional Annotation Human Genes Mouse Genes
Adaptive Immune Response 130 132
Cytokine Signaling 117 117
Inflammatory Signaling 102 103
Innate Immune Response 144 146
Microglia Function 187 187
NF-kB 60 60


Neurobiology and Neuropathology

Neuropathology research today requires a broad view of all the underlying aspects of neurological disorders and injury, including assessment of neurotransmission, neuron-glia interactions, neuroplasticity, cell integrity, neuroinflammation, and metabolism. There are 13 pathways and processes included in this panel to evaluate the impact of neuroinflammation and immune actions in the nervous system on neuropathology.

Functional Annotation Human Genes Mouse Genes
Angiogenesis 41 41
Apoptosis 140 140
Astrocyte Function 55 55
Cell Cycle 69 69
DNA Damage 82 82
Epigenetic Regulation 70 70
Growth Factor Signaling 153 153
Insulin Signaling 30 30
Matrix Remodeling 45 44
Neurons and Neurotransmission 81 80
Notch 23 23
Wnt 29 29


Metabolism and Stress

Metabolic dysfunction and stress have been shown to influence brain activity and disrupt CNS homeostasis and cognitive function by adopting neurotoxic functions. The genes selected for this panel are designed to assess important aspects of metabolism and stress that are known to impact neuroinflammation.

Functional Annotation Human Genes Mouse Genes
Autophagy 99 99
Carbohydrate Metabolism 10 10
Cellular Stress 81 81
Lipid Metabolism 18 18


Feature Specification
Number of Targets 770 (Human), 770 (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) FFPE-derived RNA, total RNA, fragmented RNA, PBMC, whole blood/plasma, iPSCs
Customizable Add up to 55 unique genes with Panel-Plus
Time to Results Approximately 24 hours
Data Analysis nSolver™ Analysis Software (RUO)


Srinivasan K, Friedman BA, Larson JL, Lauffer BE, Goldstein LD, et al. Untangling the brain's neuroinflammatory and neurodegenerative transcriptional responses. Nat Commun. 2016 Apr 21;7:11295. PubMed PMID: 27097852; PubMed Central PMCID: PMC4844685.


Holtman IR, Raj DD, Miller JA, Schaafsma W, Yin Z, et al. Induction of a common microglia gene expression signature by aging and neurodegenerative conditions: a co-expression meta-analysis. Acta Neuropathol Commun. 2015 May 23;3:31. PubMed PMID: 26001565; PubMed Central PMCID: PMC4489356.


Wang Y, Cella M, Mallinson K, Ulrich JD, Young KL, et al. TREM2 lipid sensing sustains the microglial response in an Alzheimer's disease model. Cell. 2015 Mar 12;160(6):1061-71. PubMed PMID: 25728668; NIHMSID: NIHMS661638; PubMed Central PMCID: PMC4477963.


Butovsky O, Jedrychowski MP, Cialic R, Krasemann S, Murugaiyan G, et al. Targeting miR-155 restores abnormal microglia and attenuates disease in SOD1 mice. Ann Neurol. 2015 Jan;77(1):75-99. PubMed PMID: 25381879; NIHMSID: NIHMS679333; PubMed Central PMCID: PMC4432483.


Orre M, Kamphuis W, Osborn LM, Jansen AHP, Kooijman L, et al. Isolation of glia from Alzheimer's mice reveals inflammation and dysfunction. Neurobiol Aging. 2014 Dec;35(12):2746-2760. PubMed PMID: 25002035.


Zhang Y, Chen K, Sloan SA, Bennett ML, Scholze AR, et al. An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J Neurosci. 2014 Sep 3;34(36):11929-47. PubMed PMID: 25186741; PubMed Central PMCID: PMC4152602.


Raj DD, Jaarsma D, Holtman IR, Olah M, Ferreira FM, et al. Priming of microglia in a DNA-repair deficient model of accelerated aging. Neurobiol Aging. 2014 Sep;35(9):2147-60. PubMed PMID: 24799273.


Chiu IM, Morimoto ET, Goodarzi H, Liao JT, O'Keeffe S, et al. A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model. Cell Rep. 2013 Jul 25;4(2):385-401. PubMed PMID: 23850290; NIHMSID: NIHMS499259; PubMed Central PMCID: PMC4272581.

Product Product Description Quantity Catalog Number
nCounter® Human Neuroinflammation Panel Includes 770 genes, including 13 internal reference genes for data normalization 12 Reactions XT-CSO-HNROI1-12
nCounter® Mouse Neuroinflammation Panel Includes 770 genes, including 13 internal reference genes for data normalization 12 Reactions XT-CSO-MNROI1-12

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