Chromium Single Cell CRISPR Screening

Functional genomics at single cell resolution

Study the complexity of development, disease, gene function, and therapeutic response at single cell resolution. Single cell CRISPR screens enable scalable, comprehensive readouts of cellular phenotypes directly assessing both the specific CRISPR-driven gene edits or knockdowns and the resulting perturbed gene expression profile.

Single Cell CRISPR Screening
  • Link CRISPR edits to cell phenotype

    Link CRISPR edits to cell phenotype

    Directly link CRISPR edits and gene expression phenotypes at single cell resolution.

  • Gain deeper insights

    Gain deeper insights

    Access comprehensive insights, beyond cell fitness, with single cell whole transcriptome or targeted gene expression.

  • Scale your CRISPR screens

    Scale your CRISPR screens

    Analyze genetic perturbation effects across hundreds of genes in hundreds of thousands of cells.

  • Reduce time to results

    Reduce time to results

    Quicker time to gene expression results, compared to lengthy culture times for cell survival assays.

  • Single cell resolution

    Single cell resolution

    Interrogate disease pathway and perturbation effects at scale, cell by cell.

  • Streamline data analysis

    Streamline data analysis

    Explore gene expression profiles from perturbations with easy-to-use software.

Explore what you can do

  • Scalable functional genomics

  • Unravel the drivers of differentiation and development

  • Mechanistic insights into disease biology

  • Reveal genetic contributions to disease across the entire genome

Proven results

Proven results


Watch how customers are using Chromium Single Cell CRISPR Screening.

Our end-to-end solution

Chromium instrument with Next GEM technology

Chromium instrument with Next GEM technology

Our scalable instrument

Our compact instrument

Our automated instrument

Chromium Single Cell Gene Expression reagents

Chromium Single Cell Gene Expression reagents

With our reagent kits, explore cellular diversity through 3’ mRNA, cell surface proteins, CRISPR perturbations, and more.

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.

Components required

Single Cell CRISPR Screening is enabled with the following 10x Genomics components:

Compatible products:

CRISPR Libraries

Order 10x compatible Feature Barcode CRISPR guide libraries pre-packaged in lentivirus from Sigma-Aldrich®

    CRISPR Guide Vectors

    Build your own CRISPR library by cloning sgRNAs into one of the Feature Barcode compatible vectors from AddGene:

    Single guide expression CRISPR vectors

    Dual guide expression CRISPR vector


    1. 1Step 1

      Design your CRISPR library

      Pick the target genes whose function you’d like to further investigate—from a deep dive into a focused set of tens of genes to a broad screen of hundreds of genes that comprise many pathways. Then, design your sgRNAs to order, with one of many freely available CRISPR guide RNA design tools, to clone into a 10x Genomics capture sequence enabled CRISPR vector.

    2. 2Step 2

      Prepare your sample

      Transduce and stimulate your cells—infect your cells, select the cells expressing your CRISPR guide, and apply your stimulus. Harvest your cells, and start exploring across hundreds of thousands of cells. Follow best practices for washing, counting, and concentrating cells to minimize the presence of cellular aggregates, and retrieve high-quality single cell suspensions.

    3. 3Step 3

      Construct your 10x library

      Construct a 10x barcoded library using our reagent kits and a compatible Chromium instrument. Each member of the Chromium instrument family encapsulates each cell with a 10x barcoded Gel Bead in a single partition. Within each nanoliter-scale partition, cells undergo reverse transcription to generate cDNA for both mRNA and CRISPR guides, each of which shares a 10x Barcode with all cDNA from its individual cell of origin.

      Is Single Cell CRISPR Screening compatible with Targeted Gene Expression?

      Yes, explore whole transcriptome perturbation effects or focus on pathways of interest with targeted gene expression to scale your screening throughput even further through reduced sequencing costs.

    4. 4Step 4


      Sequence the resulting 10x barcoded library on compatible standard NGS short-read sequencers for massive transcriptional profiling of hundreds of thousands of individual cells.

    5. 5Step 5

      Analyze your data

      Use our Cell Ranger analysis software to automatically assign guides on a per cell basis and directly assess perturbation effects of a guide on the target gene as well as the entire transcriptome.

      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.

    6. 6Step 6

      Visualize your data

      Interactively explore your results with our Loupe Browser visualization software. Study expression patterns for genes of interest as well as resulting perturbation phenotypes across guide targets, and perform comparative analysis between clusters and samples.

      Do I need to be a bioinformatician to use it?

      Loupe is a point-and-click software that’s easy for anyone to download and use.


    Frequently asked questions

    Single cell CRISPR screens from 10x Genomics capture and barcode CRISPR sgRNAs and cellular transcripts within each cell, providing a direct link between perturbation and phenotype in a pooled guide library format. Additionally, the readout provides information for each single cell, enabling the resolution of clusters and subpopulations of cells within a sample.

    CRISPR knockout, inhibition, and activation have all been demonstrated on 10x Genomics Chromium Single Cell Gene Expression solution with Feature Barcode technology.

    Our compatible product partner, SigmaAldrich®*, can design and manufacture custom lentiviral Feature Barcode compatible guide libraries. Feature Barcode enabled CRISPR guide vectors can also be found on Addgene, pBA900 and pBA904 deposited by the Weissman Lab.

    SigmaAldrich® 10x Genomics Custom CRISPR Lentiviral Products

    Single guide expression CRISPR vectors

    Dual guide expression CRISPR vector

    *Sigma-Aldrich is a trademark of Merck KGaA, Darmstadt, Germany or its affiliates. All other trademarks are the property of their respective owners. Detailed information on trademarks is available via publicly accessible resources.

    Gene-editing or functional genomics cores will often have resources or can help guide CRISPR guide design. Addgene also provides a guide to choosing the best CRISPR sgRNA design tool, or you can provide MilliporeSigma with your target gene list and they will design the guides for the library pool you order.

    Choosing the best CRISPR sgRNA design tool

    10x Genomics provides two types of software that will help you analyze your data: Cell Ranger and Loupe Browser. Cell Ranger is an analysis software which will automatically generate transcription profiles for each cell and determine the perturbation effects on gene expression levels. You can then use Loupe Browser, a visualization software, to interactively explore the global perturbation differences with clustering and compare differential gene expression across between perturbations. You can download Cell Ranger and Loupe Browser from the 10x Genomics Support site at no cost.

    10x Genomics Support
    Single Cell Gene Expression

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