A beginner's guide to building confidence in single cell RNA-seq
What is single cell RNA sequencing?
Single cell RNA sequencing (scRNA-seq) measures whole transcriptome gene expression in individual cells, offering a detailed view of how cells function and interact within complex tissues. Tracing individual transcripts back to their cells of origin enables researchers to pinpoint unique gene expression profiles in highly heterogeneous samples, ultimately revealing rare cell types and dynamic cell states that other methods often miss. For example, a researcher using bulk RNA-seq—which averages gene expression across many cells—to analyze a deadly tumor could miss a small population of treatment-resistant cells, potentially overlooking a putative drug target. Simply put, scRNA-seq gives you more high-quality data and deeper insights to elevate your impact.
What can single cell do for my research?
Identify disease biomarkers and mechanisms
Develop comprehensive, multiomic single cell atlases of healthy and diseased tissues to identify disease-specific cells or cell states.
Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer's disease pathology
Researchers created a cellular atlas of Alzheimer's disease, identifying markers of cognitive resilience and potential therapeutic targets for dementia.
Understand cell-specific responses in heterogeneous populations
Capture the full heterogeneity of a sample, in thousands to millions of cells.
An autocrine signaling circuit in hepatic stellate cells underlies advanced fibrosis in nonalcoholic steatohepatitis
The authors uncovered 68 receptor-ligand interactions in hepatic stellate cells, revealing their role in fibrosis in nonalcoholic steatohepatitis and identifying drug targets.
Dynamics of cellular processes
Track changes in cellular states over time to delineate developmental pathways, disease progression, and immune responses.
Transcriptional signatures associated with persisting CD19 CAR-T cells in children with leukemia
Scientists tracked leukemia patients over five years, using scRNA-seq to identify a persistent signature in long-lived CAR T cells, explaining their durable therapeutic effects.
Cell-to-cell interactions
Explore cell-cell interactions between lymphocytes and target cells in the tumor microenvironment and more.
Ovarian cancer immunogenicity is governed by a narrow subset of progenitor tissue-resident memory T cells
Cancer researchers revealed that only a small subset of tissue-resident T cells interacted with tumor cells in ovarian tumors analyzed with scRNA-seq, suggesting limited immune-tumor interaction and the need for targeted therapies.
Identify novel cell types and states
Be confident in your data with high cell recovery and sensitive detection of rare transcripts and low-RNA-content cells that often evade capture or detection with known markers.
Single-cell systems pharmacology identifies development-driven drug response and combination therapy in B cell acute lymphoblastic leukemia
Researchers discovered previously unrecognized tumor-specific cell types in lung cancer, offering insights into the molecular differences between subtypes and their prognoses.
See single cell's powerful and versatile capabilities in action
Discover how researchers across the globe have used 10x Genomics Chromium Single Cell assays to answer pressing questions across a variety of research areas.
What are the advantages of single cell RNA-seq?
| scRNA-seq | Bulk RNA sequencing | Microarray | Flow cytometry | IHC or IF | |
| Benefits | Whole transcriptome profiling at single cell resolution, rather than averaged population data Capture rare cell types and dynamic states with high-resolution insights Discover new genes, cell types, or rare populations, with increased sensitivity | Whole transcriptome profiling at the sample level, providing average gene expression across many cells Simpler workflows and analyses due to lower data complexity and resolution Lower cost and sequencing depth, with a focus on population-level insights | Quantify the expression level of specific genes of interest Examine the expression of thousands of genes simultaneously Good validation tool Cost-effective for larger studies | Measure multiple markers at once High-throughput analysis of thousands of cells per second Lowest cost per experiment | Affordable procedure that can be performed with few reagents Tissue context of gene expression |
| Challenges | Perceived higher cost vs bulk measurements Specialized analysis often required Deep sequencing is often needed to capture rare features | Population averages mask cellular heterogeneity Low resolution limits detection of rare or novel cell populations Low sensitivity misses low-level transcripts Specialized software analysis tools needed | Population-averaged results mask cellular heterogeneity Need to know genes of interest in advance High cost for a single experiment Low sensitivity and small dynamic range | Limited by predefined cell categories, determined by known cell surface proteins Expensive, specialized equipment that can be costly to maintain Data analysis can be challenging for complex samples | Specificity of antibodies can be variable (stains can be non-specific), often requiring antibody validation May be challenging to quantify results Expensive equipment needed as part of a multi-step procedure |
How can single cell RNA sequencing uniquely benefit your research?
Learn about the similarities single cell has to methods you are already familiar with while providing higher resolution insights that those methods may miss.
How can single cell enhance my research without added complexity or cost?
❌ Single cell is expensive
✅ Chromium Single Cell can be customized to your budget, without sacrificing performance
Cost is often a major barrier for new users—especially those who use bulk. But the low per-sample costs doesn't always translate to long-term savings. Without high-resolution, you could miss a new cell type or a low-level transcript key to moving your project forward (or publishing in a high-impact journal). With 10x Genomics, you get better data, fewer errors, and the confidence to get it right the first time. With costs as low as $415 USD per sample, you get high-resolution results unmatched by other single cell options, notably with up to 95% usable reads, letting you detect more genes at a lower sequencing cost. And more data doesn't mean more complexity—our free analysis pipelines require no bioinformatics experience. It's also easy to get started with a global network of 1,000+ core labs, minimizing your investment and risk.
❌ Single cell only works with fresh samples
✅ Chromium Single Cell can profile fresh, frozen, and fixed samples—even FFPE
The Chromium platform confidently tackles any research question, with more than 40 demonstrated protocols and proven performance for fresh, frozen, and fixed samples—even FFPE. Compatible sample types for Chromium Single Cell: Fresh tissue, Flow-sorted cells, Frozen tissue, Fixed human PBMCs, FFPE tissue, Fixed whole blood, PFA-fixed tissue, DSP/Methanol-fixed, Cell suspensions, Organoids, Nuclei suspensions
Explore publications utilizing a wide range of sample types
Filter for publications that conducted single analyses of your sample of interest using our database.
❌ Single cell workflows are complex and time consuming
✅ Our tried-and-tested workflows are simple, minimizing hands-on time with automation
Every experiment can be broken down into a few key steps: sample prep, running an assay, and data analysis—scRNA-seq is no different. Our optimized protocols, proven performance, instrument support, and intuitive analysis pipelines make scRNA-seq accessible for any user, no matter their experience level. Our automation instills confidence, offering superior reproducibility and time savings. We automate the most critical steps of any single cell workflow, partitioning millions of cells in minutes with just 3-4 hours of hands-on time, minimizing errors from pipetting required for manual workflows. Easily accessible via core facilities, our workflows feature a push-button interface for simplicity.
❌ Analyzing single cell data is hard—I'll have to hire or collaborate with a bioinformatician
✅ Analysis can be intuitive and easy—no expertise required
Data analysis can be hard and overwhelming, especially without bioinformatics experience. We've developed solutions that simplify the process, making it easier for researchers to process, visualize, and explore their data with our suite of user-friendly analysis tools and pipelines.
Gold-standard analysis pipelines
10x Genomics Cloud Analysis streamlines our analysis pipelines with a simple web interface that processes your data in under 90 minutes—at no cost to you.
Automated Cell Annotation
Instantly visualize cell types identified using standardized datasets, reducing the need for manual annotation and improving accuracy.
Explore your data intuitively
Loupe Browser is a powerful visualization software that provides the intuitive functionality you need to explore and analyze your data.
❌ Adopting this technology will require substantial technical training and additional resources
✅ Our end-to-end support makes getting started simple, ensuring long-term success
Our 10x Genomics technical experts provide support at every step, from experimental planning to analysis. For additional support, we offer a network of 1,000+ core facilities and a community of researchers with over 8,000 publications to rely on. You're never alone—with our in-house experts, trusted cores, and a thriving research community, you have all you need to succeed.
Set yourself up for success with expert training
Our single cell experts make starting single cell easy, with tailored training sessions for sample preparation, data analysis, and more.
Certified Service Providers
Accelerate your research with > 1,000 third-party facilities, including Certified Service Providers, who are trained and verified by 10x to support a wide variety of research applications.
Comprehensive resources for tried-and-trusted workflows
Access our collection of User Guides, Protocols, How-to Videos, Analysis Guides, and more to confidently answer your most pressing research questions, no matter the sample type or readout.
What single cell assays are available from 10x?
Flex
Protein coding gene coverage
Analyze a broad range of sample types, including FFPE and whole blood
Fix and batch flexible workflow
Customized content based on experimental need
Products
Flex
Universal
Reverse transcription–based whole transcriptome coverage
Broadest multiomic options and diverse species compatibility
Capture isoforms, long non-coding RNA, and more
Epi
Reveal the epigenomic landscape, cell by cell
Analyze chromatin accessibility at single cell resolution
Directly link gene expression and open chromatin readouts from the same nucleus
Compare assays
Compare Chromium Single Cell assays by compatible species and samples, multiomic capabilities, throughput, resolution, multiplexing options, compatible instruments, and more.