Chromium Fixed RNA Profiling

Lock in cell states, remove time constraints for gene expression

Fixed RNA Profiling provides single cell whole transcriptome gene expression and multiplexing capabilities to profile hundreds to a million cells. Fixation at the point of sample collection preserves fragile biology and greatly streamlines workflows to provide critical insights on more samples.

Fixed RNA Profiling


  • Preserve cell state

    Preserve cell state

    Fixation locks in biological states and preserves fragile or rapidly changing cells.

  • High sensitivity

    High sensitivity

    Detect low-expressing genes with high sensitivity at single cell resolution.

  • Run on your schedule

    Run on your schedule

    Remove time constraints by storing samples until you are ready to process them.

  • Built to scale

    Built to scale

    Batch and multiplex samples for a convenient workflow, cost savings, and maximum efficiency.

  • Streamlined data analysis

    Streamlined data analysis

    Explore and interpret gene expression profiles with easy-to-use software.

  • Support for sample prep

    Support for sample prep

    Make use of demonstrated protocols and guidance to optimize handling of a wide variety of sample types.

What you can do

Unlock longitudinal and larger patient cohort studies

Store samples without losing data quality, allowing you to batch multiple samples in the same run and reduce variability.

Profile tissue biopsies from the operating room

Streamline sample preparation and processing steps by locking in cell states at time of collection.

Lock and preserve rapidly changing cell states

Perform studies with short timescales, where samples change rapidly in response to a treatment or perturbation.

Differential gene expression at single cell resolution

Generate highly sensitive measurements of gene expression and cell surface proteins simultaneously.

Our end-to-end solution

Chromium X Series

Chromium X Series

Our scalable instrument for all single cell assays.

Chromium Fixed RNA Profiling kits

Chromium Fixed RNA Profiling kits

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

Analysis and visualization software

Analysis and visualization software

Our data processing platform

Our analysis pipelines

Our visualization software

World-class technical and customer support

World-class technical and customer support

Our expert support team can be contacted by phone or email at [email protected]


Scroll to see the base workflow for Fixed RNA Profiling. 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. Follow best practices for sample preparation to obtain a high-quality single cell suspension. If desired, stain cells with Feature Barcode technology to profile cell surface proteins simultaneously with gene expression.

  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.

  3. 3Step 3

    Construct your 10x library

    Hybridize the probe set to your fixed samples, and 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 the sample types tested, the Fixed RNA Profiling assay is of equal or greater sensitivity compared to that of Single Cell 3’ Gene Expression.

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 soon, mouse) samples are compatible with this assay. Start with a fresh single cell suspension and follow our fixation protocol.

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 Fixed RNA Profiling 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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