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A beginner's guide to building confidence in single cell RNA-seq

To do better science, you need better data—and single cell delivers with high-resolution insights unmatched by other methods. Our learning hub provides essential knowledge about this revolutionary research tool, empowering more researchers to conduct higher impact research.

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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.

Video: Getting Started with Single Cell Analysis

What can single cell do for my research?

10x Genomics is a proven leader in single cell research, expanding access to single cell with optimized protocols, end-to-end support, and easy-to-use analysis tools. Our technology—backed by 10 years, over 2,200 patents, and > $1.5B in R&D investment—has empowered researchers to publish over 8,000 studies, including many high-impact applications of our tools.

Stained tissue sample

Identify disease biomarkers and mechanisms

Develop comprehensive, multiomic single cell atlases of healthy and diseased tissues to identify disease-specific cells or cell states.

Featured publication

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.

Tissue sample

Understand cell-specific responses in heterogeneous populations

Capture the full heterogeneity of a sample, in thousands to millions of cells.

Featured publication

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.

Graphical representation of a cell

Dynamics of cellular processes

Track changes in cellular states over time to delineate developmental pathways, disease progression, and immune responses.

Featured publication

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.​

Digital image of cells interacting

Cell-to-cell interactions

Explore cell-cell interactions between lymphocytes and target cells in the tumor microenvironment and more.

Featured publication

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​.

Stained cells

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.

Featured publication

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.

Research journal covers

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.

Explore 8,000+ peer-reviewed publications

What are the advantages of single cell RNA-seq?

scRNA-seqBulk RNA sequencingMicroarrayFlow cytometryIHC 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

Venn diagram of different research methods

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.

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Ready to get started with single cell RNA sequencing?

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How can single cell enhance my research without added complexity or cost?

With 10x Genomics, single cell research is more accessible than ever. Our end-to-end platform simplifies every step—from sample prep to data analysis—delivering high-impact results quickly and cost-effectively. As the proven leader, we ensure unmatched data quality, so you don't risk missing critical findings, protecting both your samples and your budget.

Common misconception

Single cell is expensive

Reality with 10x Genomics Chromium Single Cell

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 $565 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.

Common misconception

Single cell only works with fresh samples

Reality with 10x Genomics Chromium Single Cell

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

Fresh tissue

Flow-sorted cells

Flow-sorted cells

Frozen tissue

Frozen tissue

Fixed human PBMCs

Fixed human PBMCs

FFPE tissue

FFPE tissue

Fixed whole blood

Fixed whole blood

PFA-fixed tissue

PFA-fixed tissue

DSP/Methanol-fixed

DSP/Methanol-fixed

Cell suspensions

Cell suspensions

Organoids

Organoids

Nuclei suspensions

Nuclei suspensions

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Explore publications utilizing a wide range of sample types

Filter for publications that conducted single analyses of your sample of interest using our database.

Explore publications

Common misconception

Single cell workflows are complex and time consuming

Reality with 10x Genomics Chromium Single Cell

Our tried-and-tested workflows are simple, minimizing hands-on time with automation

Single cell workflow diagram

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.

Learn more about our workflows, built for your success

Our automation instills confidence, offering superior reproducibility and time savings

We automate the most critical steps of any single cell workflow, partitioning thousands 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.

Learn more about our instruments

Common misconception

Analyzing single cell data is hard—I'll have to hire or collaborate with a bioinformatician

Reality with 10x Genomics Chromium Single Cell

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.

Software screenshot of Cloud Analysis

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.

Learn more about our pipeline
Software screenshot

Automated Cell Annotation

Instantly visualize cell types identified using standardized datasets, reducing the need for manual annotation and improving accuracy.

Learn more
Software screenshot of Loupe Browser

Explore your data intuitively

Loupe Browser is a powerful visualization software that provides the intuitive functionality you need to explore and analyze your data.

Explore Loupe Browser

Common misconception

Adopting this technology will require substantial technical training and additional resources

Reality with 10x Genomics Chromium Single Cell

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.

10x Genomics technical experts

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.

Speak to a specialist
A lab workbench with a number of tools for research and a 10x Genomics Chromium X instrument

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.

Find a service provider
A graphic highlighting the different aspects of a cell to be analyzed

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.

Explore support resources

What single cell assays are available from 10x?

With 10x Genomics, you can do far more than measure gene expression. Our platform offers the broadest range of solutions, enabling you to analyze the full immune repertoire, profile chromatin accessibility, and integrate transcriptomics with proteomics. As your research grows, 10x lets you expand into more advanced applications with ease. Explore an overview of our offerings below.

Ready to get started with Chromium Single Cell?

Speak to an experienced representative
Universal Gene Expression icon

Universal Gene Expression

Reverse transcription–based whole transcriptome coverage
  • Broadest multiomic options and diverse species compatibility
  • Capture isoforms, long non-coding RNA, and more
Price

As low as $565 USD per sample

Flex Gene Expression icon

Flex Gene Expression

Probe-based detection of 18,000+ coding genes
  • Analyze previously inaccessible samples, including fixed tissue and whole blood
  • Robust performance for FFPE and low-quality samples
Price

As low as $361 USD per sample

Epi Chromatin icon

Epi Chromatin

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
Price

As low as $1,528 USD per sample

Compare 10x Genomics Chromium assays

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Compare Chromium Single Cell assays by compatible species and samples, multiomic capabilities, throughput, resolution, multiplexing options, compatible instruments, and more.

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