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 phenotypes, including gene expression and cell surface proteins.

Single Cell CRISPR Screening

Resources:

  • 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 multiomic profiling.

  • 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

  • Validate hits identified in GWAS and QTL studies

  • Mechanistic insights into disease biology

  • Reveal genetic contributions to disease across the entire genome

Proven results

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Proven results

Videos

Watch how customers are using Chromium Single Cell CRISPR Screening.

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Publications

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

Nat Biotechnol. 2020, Replogle JM, et al.

Nat Biotechnol. 2020, Replogle JM, et al.

High-resolution characterization of gene function using single-cell CRISPR tiling screen

High-resolution characterization of gene function using single-cell CRISPR tiling screen

Nat Commun. 2021, Yang L, et al.

Nat Commun. 2021, Yang L, et al.

Systematic dissection of transcriptional regulatory networks by genome-scale and single-cell CRISPR screens

Systematic dissection of transcriptional regulatory networks by genome-scale and single-cell CRISPR screens

Sci Adv. 2021, Lopes R et al.

Sci Adv. 2021, Lopes R et al.

Resources

Find the latest app notes and other documentation Chromium Single Cell CRISPR Screening.

Direct capture of guide RNAs enables scalable and combinatorial single cell CRISPR screens

Direct capture of guide RNAs enables scalable and combinatorial single cell CRISPR screens

Research Snapshot, 10x Genomics

Research Snapshot, 10x Genomics

Discovering mechanisms of cancer immune evasion with multiomic single cell CRISPR screens

Discovering mechanisms of cancer immune evasion with multiomic single cell CRISPR screens

Research Snapshot, 10x Genomics

Research Snapshot, 10x Genomics

Transforming drug discovery with single cell CRISPR screens

Transforming drug discovery with single cell CRISPR screens

Infographic, 10x Genomics

Infographic, 10x Genomics

Our end-to-end solution

Chromium instrument with Next GEM technology

Chromium instrument with Next GEM technology

Chromium X Series

Our scalable instrument

Our compact instrument

Chromium Single Cell reagents

Chromium Single Cell reagents

With our reagent kits, explore cellular diversity through gene expression, 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.

Workflow

  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.

    Resources
    • CRISPR guide RNA design tools
  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.

    Resources
  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.

    Resources
  4. 4Step 4

    Sequence

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

    Resources
  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.

    Resources
  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.

    Resources

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 single cell technologies.

Our 5’ CRISPR screening assay is compatible with most pre-existing Cas9 guide RNA vectors. If you have an existing CRISPR library or are starting a single cell CRISPR screen for the first time, we recommend using our Single Cell 5’ v2 assay which is compatible with most guide libraries with little to no optimization required.

Our 3’ CRISPR screening assay requires that a specific Capture Sequence be inserted into the vector at the appropriate location for capture of the guide. If you want to compare your single cell CRISPR experiment to data from previous experiments using 3’ single cell gene expression with Feature Barcode technology, we recommend continuing to use our Single Cell 3’ v3.1 assay to minimize batch effects.

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

  • CRISPR guide vector pBA900
  • CRISPR guide vector pBA904

Dual guide expression CRISPR vector

  • CRISPR guide vector pJR85

*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
Single Cell Gene Expression

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