Multiome 10x: Complete Cell Analysis Technology
Multiome 10x is changing the game in single-cell analysis. This cutting-edge tech gives us a full picture of cellular activity by measuring gene expression and chromatin accessibility in one go1. It’s like having X-ray vision for cells, letting scientists peek into their inner workings with incredible detail.
The power of Multiome 10x lies in its versatility. It works with a wide range of samples, from cell suspensions to frozen tissue. This flexibility opens doors for researchers across different fields, from cancer studies to plant biology.
What sets Multiome 10x apart is its ability to capture data from up to 65% of loaded cells2. This high capture rate, combined with a low doublet rate, ensures reliable and comprehensive cellular insights. The technology’s compatibility with various Illumina platforms makes it a versatile tool for labs of all sizes.
Multiome 10x isn’t just about collecting data – it’s about making sense of it. The system comes with powerful analysis tools that help researchers interpret their findings. This integrated approach streamlines the workflow from sample to insight, making it easier for scientists to uncover new cellular secrets.
Key Takeaways
- Measures gene expression and chromatin accessibility simultaneously
- Works with various sample types and species
- Captures up to 65% of loaded cells
- Compatible with multiple Illumina sequencing platforms
- Includes integrated analysis tools for data interpretation
- Streamlines workflow from sample preparation to insights
What is Multiome 10x?
Multiome 10x is a groundbreaking Chromium Single Cell Multiome ATAC + Gene platform. This single-cell technology allows scientists to study both gene expression and chromatin accessibility in individual cells.
Overview of Multiome 10x
The Multiome 10x system offers unprecedented insights into cellular function. It can analyze nuclei from various species, including humans, mice, and even plants3. The technology works with different sample types, from cell suspensions to frozen tissues and organoids3.
This powerful tool can process up to 80,000 nuclei per chip, making it ideal for large-scale studies3. For a typical project targeting 10,000 nuclei, researchers need about 25,000 read pairs per nucleus for both ATAC and expression libraries4.
Key Features
Multiome 10x stands out with its versatility and high-throughput capabilities. Here are some key features:
- Compatible with various sample types and species
- High throughput options (up to 80K nuclei/chip)
- Integrates with Chromium X and iX instruments
- Requires minimal sequencing depth (20,000 read pairs for gene expression, 25,000 for ATAC)3
The technology uses specific assay components, including Chromium Nuclei Isolation kits and Next GEM Chips3. For optimal results, nuclei samples should have a concentration of 3-7.7 million nuclei/ml and viability above 80%4.
| Feature | Specification |
|---|---|
| Nuclei per sample | 500 – 10,000 |
| Nuclei per run | Up to 80,000 |
| Recommended sequencing depth | 25,000 read pairs per nucleus |
| PhiX Spike-In | 1% |
With its comprehensive approach, Multiome 10x is revolutionizing our understanding of cellular function and regulation in single-cell technology45.
Importance of Comprehensive Cell Analysis
Comprehensive cell analysis plays a vital role in advancing research across various scientific fields. The ability to examine individual cells at single-cell resolution has revolutionized our understanding of complex biological systems.
Applications in Research
Single-cell technologies have found extensive use in multiple research areas. Scientists can now perform detailed transcriptome analysis and epigenome profiling, providing unprecedented insights into cellular function and regulation. Single-cell multiomics analysis allows researchers to measure DNA, mRNA, and proteins at a single-cell resolution, offering unique perspectives on cell subpopulations and their functions in pathophysiological processes6.
These advanced techniques have proven particularly valuable in cancer research, immunology, and neuroscience. For instance, bulk multiomics analyses have shed light on cellular processes in colorectal, ovarian, breast, and gastric cancers6. The application of single-cell resolution techniques in these fields has led to the identification of rare cell types and novel biomarkers.
Benefits for Precision Medicine
The impact of comprehensive cell analysis extends beyond basic research into the realm of precision medicine. By capturing both transcriptome and epigenome simultaneously in the same single cell, researchers can gain a more holistic view of cellular function7. This detailed understanding supports the development of targeted therapies and personalized treatment approaches.
Innovative technologies like Single Cell Multiome ATAC + Gene Expression offer comparable sensitivity to standalone assays when working with nuclei7. This advancement allows for more accurate profiling of large cells like neurons, which are more easily captured in a microfluidic workflow using single nuclei7.
| Analysis Type | Key Features | Applications |
|---|---|---|
| Transcriptome Analysis | Gene expression profiling | Cancer research, Immunology |
| Epigenome Profiling | Chromatin accessibility mapping | Developmental biology, Drug discovery |
| Multiomics Analysis | Integrated DNA, RNA, and protein analysis | Precision medicine, Systems biology |
The integration of multiomic data sets using advanced analytical frameworks like MOFA and Seurat v4 enables researchers to uncover complex relationships between different molecular layers7. This comprehensive approach to cell analysis is driving significant advancements in our understanding of human health and disease, paving the way for more effective diagnostic and therapeutic strategies in precision medicine.
How Multiome 10x Works
Multiome 10x is a groundbreaking technology that combines single-cell sequencing techniques to provide a comprehensive view of cellular states. This innovative approach integrates chromatin accessibility and 3′ gene expression measurements from the same cell, offering unparalleled insights into cellular function.
Integrated Single-Cell Genomics
The Multiome 10x system utilizes advanced single nuclei RNA-seq and ATAC-seq technologies within individual cells8. This integration allows researchers to simultaneously analyze gene expression and chromatin accessibility, providing a more complete picture of cellular activity. The technology requires high-quality nuclear membranes and a specific concentration of nuclei for optimal results8.
Multi-Omics Approach Explained
The multi-omics approach of Multiome 10x involves several key steps. First, the system generates two distinct libraries per sample – one for gene expression and another for ATAC9. These libraries undergo specific read configurations during sequencing, tailored to capture both gene expression and chromatin accessibility data. The process includes full-length cDNA amplification and library construction with sample indexing8.
To ensure high-quality data, Multiome 10x recommends specific sequencing parameters. The technology is compatible with various Illumina platforms, with a preference for NovaSeq X series and NextSeq 1000/200010. After sequencing, the data undergoes analysis using specialized software like CellRanger ARC, which provides crucial metrics such as the number of cells detected and median genes per cell10.
This integrated approach allows researchers to gain deep insights into cellular function, making Multiome 10x a powerful tool for advancing our understanding of complex biological systems.
Advantages of Using Multiome 10x
Multiome 10x revolutionizes single-cell analysis by offering significant advantages in data quality, workflow efficiency, and cost-effectiveness. This innovative technology enables researchers to gain deeper insights into cellular function and regulation.
Enhanced Data Quality
Multiome 10x provides superior data quality through multimodal measurements of single cells. The platform allows for simultaneous profiling of open chromatin and gene expression from the same nuclei, offering a comprehensive view of cellular activity. This approach has shown a 27-fold enrichment of GWAS variants for inflammatory bowel disease in cis-regulatory elements, highlighting its power in uncovering disease-related insights11.
Streamlined Workflow
The technology streamlines the experimental process, enabling efficient high-throughput screening of samples. Multiome 10x’s workflow integrates various molecular data layers, allowing for comprehensive analysis of genotype-phenotype interactions. This integrated approach simplifies sample preparation and sequencing, reducing the time and complexity of multi-omics studies12.
Cost-Effectiveness
By combining multiple analyses in a single experiment, Multiome 10x offers a cost-effective solution for researchers. The platform’s ability to perform snATAC and snRNA sequencing simultaneously eliminates the need for separate experiments, saving both time and resources. This efficiency is particularly valuable in large-scale studies, where the cost savings can be substantial.
| Feature | Benefit | Impact |
|---|---|---|
| Multimodal Measurements | Comprehensive cellular analysis | Deeper insights into cell function |
| Integrated Workflow | Reduced experimental complexity | Time and resource savings |
| Single-cell Resolution | High-precision data | Improved understanding of cellular heterogeneity |
Multiome 10x’s advanced capabilities in single-cell analysis and high-throughput screening position it as a game-changing tool in biological research. Its ability to perform comprehensive, multimodal measurements at the single-cell level offers researchers unprecedented insights into cellular function and regulation13.
Use Cases in Various Fields
Multiome 10x technology has revolutionized research across multiple scientific domains. Its ability to perform single-cell profiling and analyze cellular heterogeneity has opened new avenues for understanding complex biological systems.
Cancer Research
In cancer research, Multiome 10x has proven invaluable for studying tumor heterogeneity and drug resistance mechanisms. Researchers use this technology to examine gene expression patterns and chromatin accessibility in individual cancer cells, providing insights into tumor evolution and potential treatment targets14.
Immunology Studies
Immunologists leverage Multiome 10x for deep immune profiling at scale. The technology allows for simultaneous analysis of gene expression, protein levels, and chromatin accessibility in immune cells. This comprehensive approach helps unravel the complexities of immune responses and autoimmune disorders14.
Drug Discovery
In drug development, Multiome 10x accelerates the discovery process through high-throughput screening. By analyzing cellular responses to potential drug candidates at the single-cell level, researchers can quickly identify promising compounds and optimize their efficacy15.
| Field | Application | Impact |
|---|---|---|
| Cancer Research | Tumor heterogeneity analysis | Improved understanding of drug resistance |
| Immunology | Deep immune profiling | Enhanced insights into autoimmune disorders |
| Drug Discovery | High-throughput screening | Accelerated identification of drug candidates |
The versatility of Multiome 10x extends to neuroscience, where it aids in studying complex disorders like Alzheimer’s disease and brain organoid development. This technology’s ability to capture multiple data types from single cells has transformed our understanding of cellular processes and disease mechanisms1415.
Comparing Multiome 10x to Other Technologies
The field of single-cell analysis techniques has seen significant advancements, with Multiome 10x emerging as a game-changer. This innovative technology offers unique advantages over traditional methods, revolutionizing how researchers approach cell analysis.
Traditional Methods vs. Multiome 10x
Multiome 10x stands out by providing simultaneous measurements of gene expression and chromatin accessibility in single cells. This integrated approach offers a more comprehensive view of cellular states and regulatory mechanisms compared to conventional single-cell analysis techniques16.
Unlike traditional methods that focus on one aspect of cellular function, Multiome 10x combines RNA sequencing and ATAC-seq data. This multiomics technology comparison reveals the superior capabilities of Multiome 10x in capturing a holistic picture of cellular activity16.
Performance Metrics
Multiome 10x boasts impressive performance metrics that set it apart from other single-cell analysis techniques. The technology offers high throughput capabilities, processing up to 80,000 nuclei per chip. This efficiency allows researchers to analyze large sample sizes quickly and effectively17.
Another key advantage of Multiome 10x is its compatibility with various sample types and species. This versatility makes it an invaluable tool for researchers across different fields of study. The ability to generate comprehensive multimodal data from single cells provides unprecedented insights into cellular function and behavior17.
| Feature | Traditional Methods | Multiome 10x |
|---|---|---|
| Data Integration | Limited | Seamless |
| Throughput | Varies | Up to 80K nuclei/chip |
| Sample Compatibility | Often limited | Wide range |
| Multimodal Data | No | Yes |
In conclusion, Multiome 10x represents a significant leap forward in single-cell analysis techniques. Its ability to provide integrated, high-quality data makes it an indispensable tool for researchers seeking deep insights into cellular function and behavior.
Sample Preparation Techniques
Proper sample preparation is crucial for successful Multiome 10x experiments. This section covers best practices and required equipment for optimal results.
Best Practices for Sample Handling
When preparing samples for Multiome 10x analysis, it’s essential to follow specific protocols. Tissue samples should be preserved in liquid nitrogen for future Single Cell Multiome ATAC + Gene Expression analysis, rather than at -80°C18. For nuclei samples, immediate use is necessary as they cannot be preserved18.
A clean nuclei suspension is vital for the assay to prevent chip clogging and failure18. High-quality nuclei should have well-defined edges without blebbing or disintegration, with less than 5% live cells expected after lysis18. The viability of the cell suspension should exceed 90% before nuclei isolation19.
For optimal results, aim for a maximum of 7,500 nuclei per sample to reduce the risk of overloading and increased multiplet rates19. It’s advisable to bring three times the intended number of nuclei as output for sequencing19.
Required Equipment
To ensure successful sample preparation, specific equipment is needed. Here’s a list of essential items:
- Chromium X or Chromium iX instrument
- Centrifuge
- Microscope for nuclei quality assessment
- Liquid nitrogen storage container
- Cell counter
Proper dilution of nuclei buffer is crucial for Multiome and ATAC protocols to maintain correct stock concentrations19. By following these guidelines and using the right equipment, researchers can optimize their sample preparation protocols for single-cell suspensions and nuclei isolation, ensuring high-quality data from Multiome 10x experiments1819.
Data Analysis and Interpretation
Analyzing and interpreting Multiome 10x data requires powerful software tools and expert knowledge. This section explores the available resources and the importance of collaboration in extracting meaningful insights from complex datasets.
Available Software Tools
Several software tools support the analysis of Multiome 10x data. Cell Ranger ARC stands out as a key pipeline for processing combined ATAC and gene expression data. This tool handles the unique challenges of multiome datasets, such as the wider dynamic range of gene expression compared to cut sites per peak per cell20.
Loupe Browser offers interactive visualization capabilities for both Windows and MacOS users. It allows researchers to explore their data through intuitive interfaces, making it easier to identify patterns and trends.
For those seeking quick access to analysis pipelines, Cloud Analysis provides a web-based solution. This platform enables researchers to run Cell Ranger pipelines directly from their browsers, streamlining the analysis process.
Collaborating with Bioinformaticians
Given the complexity of multiome data, collaboration with bioinformaticians is often crucial. These experts apply advanced techniques like dimensionality reduction, feature linkage, and clustering to extract meaningful insights21.
Bioinformaticians use methods such as Principal Component Analysis (PCA) for gene expression data and Latent Semantic Analysis (LSA) for ATAC data. They also perform differential enrichment analysis to identify key genes and accessible regions that distinguish cell clusters21.
| Analysis Step | Technique | Purpose |
|---|---|---|
| Dimensionality Reduction | PCA, LSA | Simplify data representation |
| Clustering | Graph-based, K-means | Group similar cells |
| Visualization | t-SNE, UMAP | Create 2D representations |
By leveraging these tools and expertise, researchers can unlock the full potential of Multiome 10x technology, gaining deeper insights into cellular function and behavior.
Case Studies and Success Stories
Multiome 10x has revolutionized single-cell multiomic profiling, enabling groundbreaking research across various fields. Let’s explore some notable success stories and customer testimonials that showcase its impact.
Research Breakthroughs
The 10x Genomics Single Cell Gene Expression solution has become a go-to tool for researchers, offering 3′ transcriptome analysis at single-cell resolution for projects requiring data from thousands of cells per sample22. This technology has been instrumental in advancing Alzheimer’s disease research and cancer studies.
A pioneering case study used Single Cell Gene Expression Flex on OCT-Embedded Patient Brain Tissue, demonstrating the ability to perform single-cell sequencing on non-fresh tissues23. This breakthrough opens new avenues for studying complex neurological disorders.
In cancer research, scientists utilized SORT-seq technology to advance a drug candidate for liver cancer, showcasing the potential of Multiome 10x in drug discovery for precancerous liver disease23. The system’s ability to analyze thousands of cells per sample at low costs per cell has made it invaluable for multi-dimensional single-cell data analysis in cancer studies22.
Customer Testimonials
Researchers praise Multiome 10x for its versatility and precision. One team working on atherosclerosis highlighted the potential of Single Cell Immune Profiling in characterizing T cells in plaques, while another utilized transcriptomes of single endothelial cells to analyze disease mechanisms23.
A scientist studying colorectal cancer remarked, “Using SORT-seq, we analyzed the immune response post-implantation of human cancer cells in zebrafish, providing crucial insights into tumor microenvironments.”23
These success stories underscore Multiome 10x’s transformative impact on single-cell multiomic profiling, advancing our understanding of complex diseases and paving the way for innovative therapies.
Future Developments and Innovations
The field of single-cell technology advancements is rapidly evolving, with exciting innovations on the horizon. Researchers are pushing the boundaries of what’s possible in cell analysis, aiming to unlock new insights into complex biological processes.
Upcoming Features
The future of multiomics innovations looks promising. The New York Genome Center’s Technology Development team is spearheading projects related to genomics and single-cell technologies, working to optimize state-of-the-art technologies for scalable workflows24. One groundbreaking development is the GEM-X Flex from 10x Genomics, which allows profiling up to 2.5 million cells per run at a cost as low as $0.01 per cell25.
Researchers are also exploring new ways to combine different analytical approaches. The ASAP-seq method, for instance, enables simultaneous profiling of accessible chromatin, protein levels, and optional capture of mitochondrial DNA in single cells26. This integration of multiple data types in a single experiment represents a significant leap forward in comprehensive cell analysis.
Adaptive Technologies
Adaptive technologies are being developed to address specific research needs. The GEM-X Universal Multiplex, for example, allows researchers to perform single cell analysis for approximately $560 per sample, with the ability to batch and run four independent samples, each containing up to 5,000 cells25. This flexibility enables scientists to tailor their experiments to their unique requirements.
Another exciting development is the DOGMA-seq method, which adapts CITE-seq for measuring gene activity across gene regulation pathways26. These advancements in multiomics innovations are paving the way for more comprehensive and nuanced understanding of cellular processes, bringing us closer to breakthrough discoveries in various fields of biological research.
Training and Support Resources
10x Genomics offers extensive resources for Multiome 10x users, ensuring smooth adoption and optimal utilization of this cutting-edge technology. The company provides comprehensive support to help researchers make the most of their single-cell analysis projects.
Online Training Options
Users can access a wealth of online training materials to enhance their skills with Multiome 10x. These resources include detailed user guides, step-by-step protocols, and instructional videos. The Multiome 10x user guides cover everything from sample preparation to data interpretation, catering to both novice and experienced users.
For those seeking in-depth data analysis training, 10x Genomics offers specialized workshops and webinars. These sessions focus on advanced techniques for interpreting multi-omics data, helping researchers extract meaningful insights from their experiments. The training programs are designed to accommodate various skill levels, ensuring that all users can benefit from the Multiome 10x platform27.
Customer Support Services
10x Genomics provides robust technical support for Multiome 10x users. Their dedicated support team assists with experimental design, troubleshooting, and data analysis challenges. Users can access this support through various channels, including email, phone, and live chat.
The company also maintains an extensive knowledge base filled with application notes, technical documentation, and sequencing recommendations. This resource allows users to find quick answers to common questions and stay updated on best practices for Multiome 10x experiments2.
With these comprehensive training and support resources, researchers can confidently leverage the power of Multiome 10x for their single-cell analysis projects, advancing their research in fields such as cancer biology, immunology, and drug discovery.
How to Get Started with Multiome 10x
Ready to dive into the world of Multiome 10x implementation? Let’s explore how you can set up your single-cell analysis with this cutting-edge technology. The journey begins with an initial consultation to tailor the process to your specific research needs.
Initial Consultation Process
To kick off your Multiome 10x implementation, reach out to 10x Genomics for a personalized consultation. Their team will assess your research goals and help design your experiment. They’ll guide you through using their Experiment Builder tool, which creates a custom list of items needed for your specific project28.
During this phase, you’ll discuss the scope of your single-cell analysis setup. The team will explain how Multiome 10x combines chromatin accessibility (ATAC) and gene expression (3′ mRNA-seq) profiling from individual cells, offering a comprehensive view of cellular function29.
Pricing and Packages
10x Genomics offers various pricing options to fit different research scales and budgets. While specific prices aren’t publicly listed, they provide customized quotes based on your project’s needs. Packages may include the single-cell Multiome kit, which contains specialized Gel Beads with oligos for both ATAC and RNA analysis29.
Remember, the full Multiome 10x setup involves more than just the kit. You’ll need to factor in costs for nuclei preparation, library generation, and sequencing. The team at 10x Genomics can help you understand the full scope of expenses and find the most cost-effective solution for your research goals.
Q&A
What is Multiome 10x?
Multiome 10x is a cutting-edge technology that performs simultaneous measurements of 3′ gene expression and chromatin accessibility from the same cell. It’s a Chromium Single Cell Multiome ATAC + Gene Expression technology that enables comprehensive profiling of the transcriptome and epigenome at single-cell resolution.
What sample types are compatible with Multiome 10x?
Multiome 10x is compatible with various sample types, including cell suspensions, nuclei suspensions, fresh tissue, frozen tissue, and organoids. It also supports multiple species, such as mouse, human, rat, non-human primate, marine, plant, and insect samples.
What are the key features of Multiome 10x?
Key features of Multiome 10x include compatibility with various sample types and species, high throughput options (up to 80K nuclei/chip), integration with Chromium X and Chromium iX instruments, and the ability to provide comprehensive insights into cellular function and regulation.
How does Multiome 10x work?
Multiome 10x works by integrating single-cell genomics techniques to simultaneously measure chromatin accessibility and 3′ gene expression from the same cell. This multi-omics approach utilizes Next GEM technology and requires specific reagents, chips, and index kits for library construction.
What are the advantages of using Multiome 10x?
Advantages of Multiome 10x include enhanced data quality through simultaneous measurement of multiple cellular features, a streamlined workflow for efficient sample processing, and cost-effectiveness by combining multiple analyses in a single experiment. It also enables highly multimodal measurements of single cells, providing deeper insights into cellular function and regulation.
In which fields has Multiome 10x been successfully applied?
Multiome 10x has been successfully applied in various fields, including cancer research, immunology, drug development, and neuroscience. It has been used to study mechanisms of action and resistance in cancer therapy, enable deep immune profiling, accelerate drug discovery processes, and investigate diseases like Alzheimer’s.
How does Multiome 10x compare to traditional single-cell analysis methods?
Multiome 10x offers advantages over traditional methods by providing simultaneous measurements of gene expression and chromatin accessibility. It has high throughput capabilities, compatibility with various sample types and species, and generates comprehensive multimodal data from single cells, providing a more integrated view of cellular states and regulatory mechanisms.
What is required for sample preparation in Multiome 10x?
Sample preparation for Multiome 10x involves specific techniques for handling various sample types. Best practices include using the Chromium Nuclei Isolation Kit for optimal nuclei suspension preparation. Required equipment includes the Chromium X or Chromium iX instrument, along with standard laboratory equipment for sample handling and processing.
What software tools are available for Multiome 10x data analysis?
Several software tools support Multiome 10x data analysis, including Cell Ranger ARC for processing Multiome ATAC + Gene Expression data, Loupe Browser for interactive visualization, and Cloud Analysis for quick access to Cell Ranger pipelines from a web browser.
What training and support resources are available for Multiome 10x users?
10x Genomics provides comprehensive training and support resources for Multiome 10x users, including online training options like user guides, demonstration protocols, and video tutorials. Customer support services offer assistance with experimental design, sample preparation, data analysis, and troubleshooting.
How can I get started with Multiome 10x?
Getting started with Multiome 10x involves an initial consultation process to assess research needs and experimental design. 10x Genomics offers various pricing and package options to suit different research scales and budgets. Interested researchers can contact 10x Genomics directly for personalized assistance and pricing information.
