Chromium Single Cell Gene Expression Flex

The gold standard for single cell RNA-seq, transformed

Chromium Single Cell Gene Expression Flex provides our most sensitive whole transcriptome profiling with ultimate flexibility, making single cell analysis possible where it wasn’t before. Uncover critical cellular insights with optimized workflows that streamline your studies and expand sample access to include fresh, PFA-fixed, and FFPE tissues.

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Single Cell Gene Expression Flex


  • Fix, batch, and run later

    Fix cells or tissue at the point of collection and batch your samples for later. Run assays on your schedule, simplify sample transport, and optimize your workflow.

  • Broad sample compatibility, including FFPE

    From fixed tissues (PFA, FFPE) to cells, nuclei, and FACS-sorted cells, even previously inaccessible samples are now easily analyzed.

  • Ultimate throughput flexibility

    Run 1 to 128 samples, or up to 1 million cells per run. Change batch and sample/cell throughput with ease.

  • Reduce per-sample costs

    Batch and multiplex to reduce per-sample costs by up to 75%, decrease sequencing cost, and maximize your resources.

  • Superior performance

    Our most sensitive whole transcriptome assay recovers more cells and detects low-expressing genes, even with challenging samples.

  • Streamlined workflow and analysis

    No optimization required. Explore gene expression profiles with robust protocols, easy data management, and rapid processing.

Simplify sample logistics

Sample fixation and storage allow for optimized and flexible sample batching while reducing variability and maintaining data quality.

Design custom probes to fit your needs

Sensitive, probe-based chemistry lets you tailor experiments to specific gene targets with user-designed probe pairs that supplement the WTA panel.

Conduct multi-site experiments

A reliable protocol preserves the biology of your precious samples, enabling research on a global scale.

Obtain high-quality data from challenging samples, even FFPE

Innovative probe design enables sensitive, robust performance, even from whole tissue, FFPE samples, and samples with fragmented RNA.

Our end-to-end solution

Chromium X Series

Our scalable instrument for all single cell assays.

Chromium Single Cell Gene Expression Flex kits

With our reagent kits, explore cellular diversity through single cell, whole transcriptome analysis of PFA-fixed or FFPE samples for human or mouse, including simultaneous measurement of cell surface proteins.

Analysis and visualization software

Our data processing platform

Our analysis pipelines

Our visualization software

World-class technical and customer support

Our expert support team can be contacted by phone or email.


Scroll to see the base workflow for Single Cell Gene Expression Flex. Options are included for sample multiplexing or use of the Feature Barcode kit for Cell Surface Protein detection.

  1. 1Step 1

    Collect your samples

    Start with tens of thousands to millions of cells. For fresh samples, follow best practices for sample preparation to obtain a high-quality single cell suspension (or skip to Step 2 to fix tissue). If desired, stain cells with Feature Barcode technology to profile cell surface proteins simultaneously with gene expression.

    For FFPE samples, follow our Demonstrated Protocol for guidance on how to dissociate FFPE tissue for use with this assay, then move directly to Step 3.

  2. 2Step 2

    Fix and permeabilize samples

    Follow our straightforward protocol to fix samples in paraformaldehyde (PFA), locking in biological states and preserving fragile cells. At this point, samples can be safely transported or stored at –80°C until you’re ready to work with them.

    If working with FFPE samples, skip this section and move directly to Step 3.

  3. 3Step 3

    Construct your 10x library

    Hybridize the probe set to your fixed samples, then perform ligation and extension reactions on the Chromium iX or X instrument to construct a 10x barcoded library. Within each nanoliter-scale partition, cells undergo RNA-templated ligation such that each resulting product shares a 10x Barcode from its individual cell of origin. For multiplexing workflows, hybridize your samples to probe sets, pool samples together, and proceed as usual—with up to 16 samples in a single lane of a Chromium chip. In this case, another unique barcode attached to each set of probes allows you to assign each individual molecule back to the sample it came from.

  4. 4Step 4


    The resulting 10x barcoded library is compatible with standard NGS short-read sequencing on Illumina sequencers for massive transcriptional profiling of hundreds of thousands of individual cells at once.

  5. 5Step 5

    Analyze and visualize your data

    Use our Cell Ranger analysis software to generate expression profiles for each cell, identify clusters of cells with similar profiles, and aggregate data from multiple samples. Interactively explore the results with our Loupe Browser visualization software.

    Analysis pipelines output

    Output includes QC information and files that can be easily used for further analysis in our Loupe Browser visualization software, or third-party R or Python tools.


Frequently asked questions

It enables the comprehensive profiling of the transcriptome (human or mouse) from single cells using a probe-based approach. The addition of Feature Barcode technology enables simultaneous profiling of cell surface protein expression for multidimensional insights into complex biology. This assay also enables sample multiplexing to increase your throughput and workflow efficiency.

In a direct comparison study, the Single Cell Gene Expression Flex assay was shown to be twice as sensitive as the Single Cell 3’ Gene Expression assay.

Fixation of samples preserves cell states, removing time constraints that can make single cell analysis challenging. The fixation protocol enables the transport of precious and/or fragile samples from the point of collection to central sites, such as core labs or service providers, for processing.

Fixation also enables greater efficiency in sample batching, which allows for more convenient workflows and reduces variability. Fixation can also neutralize infectious agents, and following proper validation of this step, samples may no longer need to be handled in a BSL-3 lab.

Human and mouse samples are compatible with this assay. Start with a fresh or frozen single cell/nuclei suspension or tissue and follow our fixation protocol, or start with FFPE tissue and follow our Demonstrated Protocol for guidance on dissociating FFPE samples for use with Single Cell Gene Expression Flex.

Cell Ranger is a set of analysis pipelines that will automatically generate expression profiles for each cell and identify clusters of cells with similar expression profiles. Subsequently, Loupe Browser, our visualization software, can be used to interactively explore the results. Both of these tools can be freely downloaded from our support site, and you can analyze 10x Genomics datasets on your own computer.

10x Genomics Cloud Analysis, currently available in the US only, will enable you to process your Single Cell Gene Expression Flex data through a simple web interface, leveraging an optimized, scalable infrastructure for fast results. Users can set up and run Cell Ranger pipelines through this cloud interface.

Single Cell Gene Expression

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