Link CRISPR edits to cell phenotype
Directly link CRISPR edits and gene expression phenotypes at single cell resolution.
Gain deeper insights
Access comprehensive insights, beyond cell fitness, with single cell whole transcriptome or targeted gene expression.
Scale your CRISPR screens
Analyze genetic perturbation effects across hundreds of genes in hundreds of thousands of cells.
Reduce time to results
Quicker time to gene expression results, compared to lengthy culture times for cell survival assays.
Single cell resolution
Interrogate disease pathway and perturbation effects at scale, cell by cell.
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
Publications
Search through many peer-reviewed publications for Chromium Single Cell CRISPR Screening.
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
Nature Biotechnology. 2020, Replogle JM, et al.
Nature Biotechnology. 2020, Replogle JM, et al.
Genome-Wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function
Genome-Wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function
Cell. 2018, Eric Shifrut, et al.
Cell. 2018, Eric Shifrut, et al.
A Genome-Wide Framework for Mapping Gene Regulation via Cellular Genetic Screens
A Genome-Wide Framework for Mapping Gene Regulation via Cellular Genetic Screens
Cell. 2019, Molly Gasperini, et al.
Cell. 2019, Molly Gasperini, 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
Resolving the transcriptional events of life’s earliest stages with CRISPR and single cell RNA-sequencing
Resolving the transcriptional events of life’s earliest stages with CRISPR and single cell RNA-sequencing
Blog Article, 10x Genomics
Blog Article, 10x Genomics
Our end-to-end solution
Chromium instrument with Next GEM technology
Our scalable instrument
Our compact instrument
Our automated instrument
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
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.
Components required
Single Cell CRISPR Screening is enabled with the following 10x Genomics components:
- Chromium Next GEM Single Cell 3' Kit v3.1
(1000269, 4rxns | 1000268, 16rxns)
- Chromium Next GEM Single Cell 3’ HT Kit v3.1
(1000370, 8rxns | 1000348, 48 rxns)
- 3’ Feature Barcode Kit
(1000262, 16rxns)
- Chromium Next GEM Chip G Single Cell Kit
(1000127, 16rxns | 1000120, 48 rxns)
- Dual Index Kit TT Set A
(1000215, 96 rxns) - Gene Expression Libraries
- Dual Index Kit NT Set A
(1000242, 96 rxns) - CRISPR Feature Barcode Libraries
- Targeted Gene Expression
- 3' CellPlex Kit Set A
(1000261, 48 rxns)
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
Workflow
- 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.
Resources - 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
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- User Guide / Protocol
HT User Guide / Protocol - Coming Soon
- 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
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
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 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.
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.
