Glowing stem cells intertwining with a NanoString nCounter device, symbolizing precision and groundbreaking discoveries.

Unlock the Secrets of Your Stem Cells: A Simple Guide to NanoString Technology

Kai Mendoza in Science & Nature June 2025 • 3 min read.

"Mastering Stem Cell Research: How NanoString's nCounter System Simplifies Marker Expression Analysis"

Stem cells, with their remarkable ability to develop into various cell types, hold immense promise in modern medicine. Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) are now fundamental in studying neuronal development, understanding how our bodies work, modeling diseases, and pioneering new therapies. However, working with these cells isn't always straightforward. Their characteristics can change, making it crucial to regularly check whether they maintain their original state or have started to differentiate into more specialized cells, like neural progenitor cells (NPCs).

Traditionally, scientists have used specific antibodies to detect transcription factors—proteins that control gene activity—to confirm the identity of stem cells. This involves testing for proteins present in ESCs but absent in NPCs. Yet, this method can be time-consuming and expensive. The NanoString nCounter system offers a quicker, more efficient alternative. It allows researchers to measure the expression levels of key transcription factors, providing valuable insights into the state of stem cell cultures.

This guide will walk you through using the NanoString nCounter system, explaining its advantages, the materials you'll need, and a step-by-step protocol. Whether you're an experienced researcher or new to stem cell technology, this resource will equip you with the knowledge to effectively monitor and characterize your stem cell cultures.

Decoding Stem Cells with NanoString: A Step-by-Step Guide

Glowing stem cells intertwining with a NanoString nCounter device, symbolizing precision and groundbreaking discoveries.

The NanoString nCounter system offers a streamlined approach to analyzing stem cell marker expression. This system allows researchers to directly measure the levels of specific RNA molecules in a sample, providing a quantitative assessment of gene expression. Here’s how it works:

First, a unique barcode is designed to target specific RNA sequences of interest. This barcode hybridizes to the RNA in your sample. Next, a capture probe with a biotin label binds to the complex. The biotin allows the complex to be isolated and prepared for analysis. Finally, the nCounter system counts the number of barcodes present, giving you a precise measurement of each target RNA's abundance.

Speed and Efficiency: The nCounter system reduces the time and resources needed for stem cell characterization, providing results much faster than traditional methods.
Cost-Effectiveness: By multiplexing targets (measuring multiple genes simultaneously), the nCounter system reduces overall costs.
Flexibility: This platform is adaptable to various stem cell lineages and can be customized to monitor different transcripts.

Ready to get started? Here’s a simplified protocol to help you begin using the NanoString nCounter system in your stem cell research:

Empowering Your Research

The NanoString nCounter system is a powerful tool for any researcher working with stem cells. By simplifying the process of marker expression analysis, this technology enables more efficient and reliable stem cell characterization. As stem cell research continues to advance, tools like the nCounter system will play a crucial role in unlocking new discoveries and therapies. Embrace this technology to enhance your research and contribute to the exciting future of stem cell medicine.

About this Article -

This article was crafted using a human-AI hybrid and collaborative approach. AI assisted our team with initial drafting, research insights, identifying key questions, and image generation. Our human editors guided topic selection, defined the angle, structured the content, ensured factual accuracy and relevance, refined the tone, and conducted thorough editing to deliver helpful, high-quality information.See our About page for more information.

This article is based on research published under:

DOI-LINK: 10.1007/978-1-4939-8805-1_5, Alternate LINK

Title: Detecting Stem Cell Marker Expression Using The Nanostring Ncounter System

Journal: Methods in Molecular Biology

Publisher: Springer New York

Authors: Scott Ryall, Anthony Arnoldo, Javal Sheth, Sheila K. Singh, Cynthia Hawkins

Published: 2018-10-16

Everything You Need To Know

How does the NanoString nCounter system work in simplifying stem cell marker expression analysis?

The NanoString nCounter system revolutionizes stem cell research by directly measuring RNA molecules, eliminating the need for traditional, time-consuming methods. It utilizes unique barcodes that hybridize to specific RNA sequences. Capture probes with biotin labels then bind to the complex, allowing isolation and preparation for analysis. The nCounter system then counts the barcodes, providing a precise measurement of each target RNA’s abundance.

What are the key benefits of using the NanoString nCounter system for stem cell research, compared to traditional methods?

The NanoString nCounter system offers several advantages for stem cell researchers. It provides speed and efficiency, reducing time and resources needed for stem cell characterization. It also offers cost-effectiveness through multiplexing targets (measuring multiple genes simultaneously) to reduce overall costs. It provides flexibility, making it adaptable to various stem cell lineages and can be customized to monitor different transcripts.

Why is measuring transcription factor expression important in stem cell research, and how does the NanoString nCounter system help?

Transcription factors are proteins that control gene activity, and measuring their expression levels is crucial for confirming the identity and state of stem cells. Specifically, researchers often test for proteins present in Embryonic Stem Cells (ESCs) but absent in Neural Progenitor Cells (NPCs). Traditional methods of detection, like using specific antibodies, are often time-consuming and expensive. The NanoString nCounter system offers a quicker, more efficient alternative for measuring the expression levels of these key transcription factors.

What are Embryonic Stem Cells (ESCs) and induced Pluripotent Stem Cells (iPSCs), and why is it important to monitor their state using tools like the NanoString nCounter system?

Embryonic Stem Cells (ESCs) and induced Pluripotent Stem Cells (iPSCs) are valuable tools, used in studying neuronal development, understanding how our bodies work, modeling diseases, and pioneering new therapies. However, stem cells can change their characteristics over time, potentially differentiating into more specialized cell types like Neural Progenitor Cells (NPCs). This makes it important to regularly assess whether they maintain their original state, which can be achieved by using tools such as the NanoString nCounter system.

How does the NanoString nCounter system contribute to advancements in regenerative medicine, and what other considerations are important for comprehensive stem cell analysis?

The NanoString nCounter system contributes significantly to the advancement of regenerative medicine by simplifying and accelerating the characterization of stem cells. By allowing researchers to quickly and reliably determine the state and identity of stem cells, the nCounter system helps to ensure the quality and consistency of stem cell cultures used in research and potential therapeutic applications. This accelerates the discovery of new therapies and improves the prospects for successful clinical outcomes in stem cell-based treatments. However, it's important to note that while this system provides valuable data on gene expression, a comprehensive understanding of stem cell behavior often requires integrating this data with other analytical techniques, such as flow cytometry and functional assays.