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.
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 tens 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
Watch how customers are using Chromium Single Cell CRISPR Screening.
Search through many peer-reviewed publications for Chromium Single Cell CRISPR Screening.
Find the latest app notes and other documentation Chromium Single Cell CRISPR Screening.
Our End-to-End Solution
Chromium Instrument with Next GEM technology
Our compact instrument
Chromium Single Cell Gene Expression Reagents
With our reagent kits, explore cellular diversity through 3’ mRNA, CRISPR perturbations, and more.
Analysis and Visualization Software
Our analysis pipelines
Our visualization software
World-Class Technical and Customer Support
Our expert support team can be contacted by phone or email.
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)
- 3’ Feature Barcode Kit
- 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
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:
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
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 tens 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
Construct your 10x library
Construct a 10x barcoded library using our reagent kits and Chromium Controller. The Chromium Controller 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 THIS 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. Learn moreResources
Sequence the resulting 10x barcoded library on compatible standard NGS short-read sequencers for massive transcriptional profiling of thousands of individual cells.Resources
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
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