Application
Single-Cell Analysis
Single-cell analysis studies individual cells to uncover heterogeneity within complex tissues, unlike bulk methods that average signals. It combines technologies such as single-cell genomics, transcriptomics, epigenomics, proteomics, and metabolomics. Together, these tools form what’s known as single-cell multi-omics—an integrated approach that reveals the full complexity of cellular systems.
Applications include understanding cellular diversity, identifying rare cell types, mapping gene expression, chromatin accessibility, and protein or metabolite profiles to link genotype to phenotype and guide experimental design.
Among the technologies used in single-cell analysis, single-cell sequencing, based on Next-Generation Sequencing (NGS) or Third-Generation Sequencing (TGS), is one of the most widely used approaches for profiling individual animal and human cells at high resolution.
Researchers can choose from multiple partitioning strategies depending on their application. Partitioning methods include droplet-based platforms (e.g., 10x Genomics Chromium X, BD Rhapsody), reagent-based approaches like split-pool barcoding (e.g., Parse Evercode) or PIP-based workflows (e.g., Illumina).
How Hamilton Supports Your Single Cell Analysis Workflows
Hamilton supports key steps in the single-cell multi-omics workflow, from sample storage to library preparation. Our automated storage solutions ensure safe and efficient sample management across a range of temperatures and formats.
In library preparation, Hamilton works closely with leading technology providers to co-develop biologically validated protocols, implemented on our NGS Assay Ready Workstations, automated systems designed to streamline NGS applications.
The NGS STAR MOA enables fully automated, walk-away workflows for single-cell RNA sequencing (scRNA-seq), single-cell multi-omics, and conventional short- and long-read sequencing. This reduces hands-on time and increases throughput, helping researchers achieve consistent, high-quality results with greater efficiency.
Explore our Single-Cell Level Solutions and Applications in Detail
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The Hamilton Microlab Prep is an affordable liquid handler perfect for automating workflows. This entry-level liquid handler supports automated PCR setup and serial dilution.
The Hamilton Microlab STAR is a reliable and versatile automated liquid handling platform. With advanced features like multi-probe heads, pipetting technologies, and VENUS software, this premier liquid handling system fits your laboratory needs. Revolutionize your workflows with the STAR today!
Hamilton STAR V, a cutting-edge liquid handling robot, unites Microlab STAR flexibility with Microlab VANTAGE high-performance capabilities to boost efficiency. The Microlab STAR V offers speed, precision, and technology for automated liquid handling. Upgrade your lab—explore the Microlab STAR V!
Hamilton VANTAGE 2.0 is a cutting-edge liquid handling system with automated precision. Optimize workflows with the VANTAGE robot, all while boosting performance, safeguarding samples, and maximizing walk-away time. Discover the Hamilton VANTAGE liquid handler for your current & future needs.
Ambient, +4°C, -20°C Sample Storage
Verso Q-Series
Verso Q-Series automated freezer storage systems allow you to spend less time managing your samples. Verso Q20, Verso Q50, and Verso Q75 automated ambient to minus 20°C freezers feature large storage capacities in extremely compact footprints.
Ambient, +4°C, -20°C Sample Storage
Verso
Hamilton Verso is a modular compound management system for automated storage at temperatures from ambient to minus 20°C for high-throughput applications. This compound and sample storage system can easily be configured to meet your needs.
-80°C Sample Storage
SAM HD Pro
The SAM HD Pro lab freezer is your solution for high-density storage with a small footprint. This compact lab freezer is capable of ultra-low temperatures down to minus 80°C to ensure sample integrity. The SAM HD Pro sample freezer makes automated storage quick and easy.
-80°C Sample Storage
BiOS
BiOS is Hamilton’s premier minus 80°C freezer for medium- and large-capacity storage. This ultra-low temperature freezer maintains the integrity of your biological sample storage throughout automation. With customizable size and capacity, this minus 80°C freezer can be scaled to fit your storage needs.
Assay Ready Workstations
NGS STAR Line
Hamilton NGS STAR helps streamline next-generation sequencing in labs. Achieve full NGS automation for library prep, optimized for NGS assays and genome sequencing. Enhance efficiency, precision, and reliability in your workflows. Explore the Hamilton NGS STAR for seamless sequencing today!
Microliter Syringes
7000 Series Microliter Syringes
The 7000 series syringes are considered modified Microliter syringes for their unique design. This series of syringes is ideal for dispensing volumes from 0.05 μL up to 5 μL. The 7000 series is the only zero dead volume syringe.
Lab Syringes
Gastight Syringes
The solution for dispensing both gases and heterogeneous liquids. Hamilton Gastight syringes are equipped with a precision-machined PTFE plunger tip to create a leak-free seal.
Lab Syringes
Syringe Accessories
Hamilton offers a wide range of syringe accessories to improve functionality and reproducibility of a syringe. From repeated dispensers and plunger accessories to cleaning products and solutions, we have you covered.
Good to Know About Single Cell Analysis Workflows
This section provides a selection of additional resources related to the application described on this page. It includes helpful articles, videos, and blogs that offer deeper insights into the topic.
Useful Links
External resources not written by Hamilton but valuable for understanding the topic, such as industry guidelines, explanatory videos, or relevant tools.
Technology providers often feature introductory guides and resources for beginners, such as:
| Getting Started with scRNA-seq: Experimental Design and Sample Preparation - Parse Bioscience | Read Article |
| Scalable Single Cell Sequencing Without the Instrument | Evercode split-pool combinatorial barcoding - Parse Bioscience | Watch Video |
| A beginner's guide to building confidence in single cell RNA-seq - 10x Genomics | Visit Website |
| How it Works | Chromium Single Cell Gene Expression Solution - 10x Genomics | Watch Video |
| BD Rhapsody™ HT Single-Cell System - BD | Watch Video |
Review article:
| Lee, J., Hyeon, D. Y., & Hwang, D. (2020). Single-cell multiomics: Technologies and data analysis methods. Experimental & Molecular Medicine, 52, 1428–1442. | Read Article |
Solutions for the Top 3 Challenges for Single-Cell RNA Library Prep Workflows
Achieving high reproducibility and precision in low-volume pipetting.
Challenge: Consistent, high-quality libraries depend on precise, low-volume liquid handling.
Solution: Hamilton automation platforms are designed to support your lab’s success by delivering precision at every step. Our patented Compressed O-Ring Expansion (CO-RE) system ensures secure, airtight tip attachment for accurate and reproducible pipetting, reducing sample loss and variability. Total Aspiration and Dispense Monitoring (TADM) provides real-time monitoring to detect deviations during pipetting.
Additionally, VeriPlate and the Hamilton Pipetting Excellence Program (HPEP) enable routine verification of volume accuracy, supporting reliable high-throughput library preparation and robust, reproducible results.
Temperature control for sensitive reactions
Challenge: RNA molecule handling and enzymatic reactions require precise thermal conditions to maintain sample integrity and reaction efficiency.
Solution: Hamilton integrated thermal solutions help ensure consistent results in temperature-sensitive workflows. The on-deck thermal cycler provides precise temperature control directly on the platform to support critical steps like reverse transcription and PCR. Additional heating and cooling modules, as well as CELSORA, a temperature and humidity monitoring module, complete Hamilton offerings for accurate temperature control in sensitive workflows.
Scalability and Sample Tracking
Challenge: Managing large sample volumes and ensuring traceability can be challenging, error-prone, and often beyond manual capabilities.
Solution: Automating your single-cell workflows enhances consistency, scalability, and traceability, all while reducing manual touchpoints. Hamilton offers automation solutions tailored to various sample throughput needs and integrates barcode scanning modules for sample identification and complete process traceability. With walk-away automation, researchers can streamline complex workflows, reduce manual intervention, and focus on data analysis rather than process management.
What Is Single-Cell Analysis?
Single-cell analysis approaches (e.g. scRNA-seq) and technologies from industry leaders like Becton Dickinson and 10x Genomics have significantly enhanced genomic studies to advance our understanding of cellular diversity and function.
Think of bulk sequencing like a smoothie, where the cellular contents are blended, and individual contributions are lost. While this method can work well in highly uniform cell populations or when comparing broad differences between conditions, it lacks the precision needed to resolve complexity.
In contrast, single-cell analysis is like a fruit salad; you can distinguish each component clearly. Here, you get a more detailed and precise profile of individual and specific cells within a sample, eliminating the need for guesswork and assumptions. With this level of granularity, researchers can confidently explore cell states, track developmental pathways, and drive insights that fuel discovery.
What Are Single Cell Transcriptomics?
Single-cell transcriptomics studies gene expression at the individual-cell level, offering insights that bulk RNA sequencing cannot provide. Unlike bulk RNA-seq methods, single-cell RNA sequencing (scRNA-seq) captures each cell’s unique gene expression profile. This technique reveals details about cell type, state, and function, especially in complex tissues like tumors and the immune cell repertoire.
Using high-throughput methods, scientists analyze thousands of cells at once. Advanced computational tools help classify distinct cell types and identify differentially expressed genes (i.e., genes that show variation across cell populations or conditions).
Single-cell transcriptomics is essential for detecting rare or transient cell types and for monitoring cellular shifts over time. These insights not only deepen biological understanding, but also guide downstream experimental design, therapeutic targeting, and biomarker discovery.
Benefits of Single Cell Analysis Applications
Single-cell analysis enables precise insights by studying individual cells, offering a resolution far beyond bulk sequencing methods, which average signals across populations. scRNA-seq offers higher resolution and is capable of:
- Unmasking cellular heterogeneity
- Identifying rare cell populations
- Understanding dynamic cell states
These approaches offer transformative advantages for both research institutions and service providers, especially when paired with Hamilton automated solutions for throughput, reproducibility, and data integrity. Applications span across diverse fields, including:
- Assessing tumor heterogeneity and cell type variation
- Revealing immune cell response and autoimmune disease processes
- Characterizing microbial strains and investigating infectious disease processes
- Understanding developmental processes and disorders
- Advancing vaccine and cell therapy development
- Performing high-throughput cell-based assay screenings
- Creating cell atlas databases for different tissues and species
With Hamilton enabling technologies, scientists can confidently scale their single-cell research, turning granular data into breakthrough discoveries.
Other Single Cell Analysis Resources
Browse app notes, user guides, specification documents, and more in our Knowledge Center.
Browse app notes, user guides, specification documents, and more in our Knowledge Center.
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