nCounter® Stem Cell Characterization Panel

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Helping Your Research

Stem cell therapy is a rapidly advancing field with applications across a broad range of research areas including neuroscience, cardiology, autoimmunity, ophthalmology, and oncology. Deeply characterize and optimize your stem cell development with the nCounter Stem Cell Characterization Panel. This panel measures the eight essential components of stem cell biology. Evaluate viability, confirm functionality and determine pluripotency with a single robust, automated, and reproducible assay. Assess stem cell health during production and easily detect contamination to quickly optimize cell culture conditions and expedite your research.

How it Works


Directly profile 770 genes involved in stem cell biology

  • Stemness
  • Pluripotency
  • Regulatory Signaling
  • Epigenetics
  • Mechano-Signaling
  • Metabolism
  • Differentiation Signaling
  • Lineage Specification

Characterize stem cells during development

  • Confirm pluripotency
  • Understand reprogramming failures
  • Assess activation/differentiation status

Screen for viability


Confirm expanded cell function via cell signaling and activation pathways


Confirm cell viability after gene editing


Detect mycoplasma contamination


Generate data in 24 hours with less than 30 minutes hands on time and simple data analysis

Stem Cell Therapy Workflow

Culturing stem cells is a delicate art. The environment needs to be tightly controlled and the cells need to be checked at each stage to ensure that they are differentiating as desired. The Stem Cell Characterization Panel can be used throughout development processes to confidently characterize stem cells and understand pluripotency.

Contamination Detection

Mycoplasma is a common contaminant in cultured cells. Mycoplasma compete with stem cells for nutrients and can have a profound impact on global gene expression levels within the cells. The Stem Cell Characterization panel contains a probe to detect mycoplasma, allowing for quick and easy detection of culture contamination.

Customization with Panel Plus

Customize your research project by adding up to 55 user-defined genes of interest with nCounter® Panel Plus. Panel Plus capacity enables researchers to address areas like specific lineage interests, such as cardiomyocytes, neurons, retinal cells and beta cells.

Data Analysis

In addition to the standard nSolver™ Analysis Software, genes included in the Stem Cell Characterization panel are organized and linked to various advanced analysis modules to allow for efficient analysis of relevant pathways.

Advanced Analysis Modules available for Stem Cell Characterization:

  • Normalization
  • Quality Control
  • Individual Pathway Analysis
  • Differential Expression
  • Gene Set Analysis
  • Built-in compatibility for Panel-Plus and Protein analysis

Data can also be analyzed using ROSALIND®. ROSALIND is a cloud-based platform that enables scientists to analyze and interpret differential gene expression data without the need for bioinformatics or programming skills.

Rosalind Guided Module available for Stem Cell Characterization:

  • Normalization
  • Quality Control
  • Individual Pathway Analysis
  • Differential Expression
  • Gene Set Analysis

Panel Selection Tool

Find the gene expression panel for your research with Panel Pro

Find Your Panel


View all publications

Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution

Conventional human embryonic stem cells are considered to be primed pluripotent but can be induced to enter a naive state. However, the transcriptional features associated with naive and primed pluripotency are still not fully understood.

The interplay of epigenetic marks during stem cell differentiation and development

Chromatin, the template for epigenetic regulation, is a highly dynamic entity that is constantly reshaped during early development and differentiation. Epigenetic modification of chromatin provides the necessary plasticity for cells to respond to environmental and positional cues, and enables the maintenance of acquired information without changing the DNA sequence.

StemCellDB: the human pluripotent stem cell database at the National Institutes of Health

Much of the excitement generated by induced pluripotent stem cell technology is concerned with the possibility of disease modeling as well as the potential for personalized cell therapy. However, to pursue this it is important to understand the ‘normal’ pluripotent state including its inherent variability.

Pluripotent Stem Cell-Based Cell Therapy-Promise and Challenges

Human pluripotent stem cells such as embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) provide unprecedented opportunities for cell therapies against intractable diseases and injuries. Both ESCs and iPSCs are already being used in clinical trials.

Lessons from human teratomas to guide development of safe stem cell therapies

The potential for the formation of teratomas or other neoplasms is a major safety roadblock to clinical application of pluripotent stem cell therapies. Preclinical assessment of the risk of tumor formation in this context poses considerable scientific and regulatory challenges, especially because animal xenograft models may not properly reflect the long-term tumorigenic potential of human cells.

Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors

Differentiated cells can be reprogrammed to an embryonic-like state by transfer of nuclear contents into oocytes or by fusion with embryonic stem (ES) cells. Little is known about factors that induce this reprogramming.

Induced pluripotent stem cell technology: a decade of progress

Since the advent of induced pluripotent stem cell (iPSC) technology a decade ago, enormous progress has been made in stem cell biology and regenerative medicine. Human iPSCs have been widely used for disease modelling, drug discovery and cell therapy development.

Dynamic stem cell states: naive to primed pluripotency in rodents and humans

The molecular mechanisms and signalling pathways that regulate the in vitro preservation of distinct pluripotent stem cell configurations, and their induction in somatic cells by direct reprogramming, constitute a highly exciting area of research. In this Review, we integrate recent discoveries related to isolating unique naive and primed pluripotent stem cell states with altered functional and molecular characteristics, and from different species.

Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells

We examined the gene expression and DNA methylation of 49 human induced pluripotent stem cells (hiPSCs) and 10 human embryonic stem cells and found overlapped variations in gene expression and DNA methylation in the two types of human pluripotent stem cell lines. Comparisons of the in vitro neural differentiation of 40 hiPSCs and 10 human embryonic stem cells showed that seven hiPSC clones retained a significant number of undifferentiated cells even after neural differentiation culture and formed teratoma when transplanted into mouse brains.

Concise review: The evolution of human pluripotent stem cell culture: from feeder cells to synthetic coatings

Current practices to maintain human pluripotent stem cells (hPSCs), which include induced pluripotent stem cells and embryonic stem cells, in an undifferentiated state typically depend on the support of feeder cells such as mouse embryonic fibroblasts (MEFs) or an extracellular matrix such as Matrigel. Culture conditions that depend on these undefined support systems limit our ability to interpret mechanistic studies aimed at resolving how hPSCs interact with their extracellular environment to remain in a unique undifferentiated state and to make fate-changing lineage decisions.

Related Resources

Product Bulletin nCounter® Stem Cell Characterization Panel Product Bulletin
Webinar A Brief nCounter virtual experience with the Stem Cell Characterization Panel
Blog Post Pluripotent Stem Cells: How to Best Use Them in Your Research
Event Enhancing Stem Cell Research with the NEW nCounter® Stem Cell Characterization Panel
Manual/Instructions NanoU Training Videos

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The Stem Cell Characterization Panel provides a comprehensive view of a stem cell’s life cycle. Probes cover all eight essential components of stem cell biology.

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