Products & Services
PRCISR™ CRISPR libraries, screening & computational services
Consulting
Products
Screening
Bioinformatics
Vivlion’s CRISPR-enabled Discovery Platform
Vivlion offers pooled and arrayed PRCISR™ CRISPR libraries, screening services and bioinformatic analysis. Screening services are offered alongside a detailed consultation for your experimental strategy and design. Our PRCISR™ CRISPR discovery platform delivers your required data in a highly efficient and integrated process.
Vivlion’s services are modularly organized, each representing a distinct phase of your CRISPR screening project.
Experimental design: critical parameters of the experimental setup are discussed, such as the biological question, cellular context, control concept, including the library design and format – whether to use a library that is readily available from Vivlion or a library specifically tailored to your experiment, is agreed.
Library production: in the case of a tailored PRCISR™ CRISPR library, the production time takes up to six weeks, whereas off-the-shelf PRCISR™ CRISPR libraries are available within four weeks. The library can be delivered as plasmid DNA. If Vivlion carries out the CRISPR screen, Vivlion undertakes viral library production and titration.
CRISPR screening and analysis contains distinct stages: Cell line QC confirms cell line identity and tests for contamination. Then cells are expanded to the required scale. Screening takes up to six weeks and is performed according to the agreed experimental design, such as readouts, treatments and duration. Samples are subjected to next-generation sequencing (NGS). Data analytics entails NGS quality control and phenotypic hit calling.
Optionally, Vivlion offers to enrich the resulting experimental data by further data integration.
Experimental design for successful screening projects
Vivlion consults in the following areas:
- gene editing and replacement requirements
- screening projects and their demands
- library design and gRNA formats
- target and control sequences
- nuclease selection and delivery formats
- NGS and data analyses workflows
- CRISPR workflows and facilities
Vivlion offers to consult with you on your screening projects. Please reach out on our contact form to request our customer questionnaire outlining the parameters for library design and desired screen outcome for your experiments.
PRCISR™ CRISPR libraries
Vivlion’s PRCISR™ CRISPR libraries are offered in single, fixed-pair and dual-multiplex formats. We have a range of libraries that are readily available – in addition, Vivlion can provide PRCISR™ CRISPR libraries specifically tailored to your requirements.
PRCISR™ CRISPR libraries address a range of challenges in CRISPR screening, including applications utilizing sparse cell material, high-volume CRISPR screens and large combinatorial CRISPR screens. The uniformity of our libraries enable
- experimental downscaling (10x)
- parallelization of screening projects
- iterative and parallell combinatorial screens (> 6M gene pairs)
Single
Single libraries deliver single gRNAs per cell. Our PRCISR™ CRISPR technology uncouples sequence diversity from distribution, thereby enabling all sequence diversities.
Fixed-pair
Fixed-pair libraries deliver pre-defined gRNA pairs per cell in all sequence diversities. On-target rates can be improved and applications like paralog exploration and DNA excision are enabled.
Dual-multiplex
Dual-multiplex libraries deliver combinations of two gRNAs per cell, enabling the exploration of combinatorial gene effects, e.g. functional buffering, synthetic vulnerabilities and genetic interactions.
–
| Single library | Fixed-pair library | Multiplex library | ||||
|---|---|---|---|---|---|---|
| PRCISRTM CRISPR | Conventional PCR library | PRCISRTM CRISPR | Conventional PCR library | PRCISRTM CRISPR | Conventional PCR library | |
| CRISPR application | Single edits | Single edits | Dual edits | Dual edits | Dual edits | Dual edits |
| Coverage | 50-100 | 500-1000 | 50-100 25-50 (same target) |
500-1000 250-500 (same target) |
50-100 | 500-1000 |
| Skew | <2 | >>2 | <2 | >>2 | <2 | >>2 |
| Hit retention rate | high | low | high | low | high | low |
| Culture flasks need | 4 per genome-wide screen | 40 per genome wide screen | 4 per genome-wide screen (2 for same target) | 40 per genome-wide screen (20 for same target) | Depending on diversity | Depending on diversity |
| Available libraries | Please, contact us for product list | See 3rd party providers | Please, contact us for product list | See 3rd party providers | Customized | |
Single Library
| PRCISRTM CRISPR | Conventional PCR library | |
|---|---|---|
| CRISPR application | Single edits | Single edits |
| Coverage | 50-100 | 500-1000 |
| Skew | <2 | >>2 |
| Hit retention rate | high | low |
| Culture flasks need | 4 per genome-wide screen | 40 per genome-wide screen |
| Available libraries | Please, contact us for product list | See 3rd party providers |
Fixed Pair Library
| PRCISRTM CRISPR | Conventional PCR library | |
|---|---|---|
| CRISPR application | Dual edits | Dual edits |
| Coverage | 50-100 25-50 (same target) |
500-1000 250-500 (same target) |
| Skew | <2 | >>2 |
| Hit retention rate | high | low |
| Culture flasks need | 4 per genome-wide screen (2 for same target) | 40 per genome-wide screen (20 for same target) |
| Available libraries | Please, contact us for product list | See 3rd party providers |
Multiplex Library
| PRCISRTM CRISPR | Conventional PCR library | |
|---|---|---|
| CRISPR application | Dual edits | Dual edits |
| Coverage | 50-100 | 500-1000 |
| Skew | <2 | >>2 |
| Hit retention rate | high | low |
| Culture flasks need | Depending on diversity | Depending on diversity |
| Available libraries | Customized |
Featured PRCISR™ CRISPR libraries
ALEXANDRIA: Vivlion’s flagship fixed-pair genome-wide PRCISR™ CRISPR library.
Industry-leading uniformity, efficiency and gene coverage.Targets 20,381 genes (99.8% of all ENSEMBLE-identified genes)
Diversity of 40k: 4 gRNAs per gene, 2 pairs per gene
gRNAs selected for highest activity
Innovative screening quality control concept
Data sheet and handling protocols available on request.
coming soon – PERGAMON: A minimized fixed-pair genome-wide PRCISR™ CRISPR library.
Industry-leading uniformity, efficiency and gene coverage.Targets 20,256 genes (99.1% of ENSEMBLE-identified genes)
Diversity of 20k: 2 gRNAs per gene, 1 pair per gene
gRNAs selected for highest activity
Innovative screening quality control concept
Data sheet and handling protocols available on request.
PRCISR™ CRISPR screening services
Vivlion offers screening services with a variety of library delivery methods and screening setups. Tailored to the cellular context of interest, the gRNA library can be delivered with lentiviral, retroviral and recombinant adeno-associated virus. A viability screen without any treatment is useful to identify essential genes in a given context and serves as a control for more complicated experiments that include the application of selection pressures. A positive selection pressure helps identify resistance factors in cells that tolerated and survived the treatment while a negative selection enables finding sensitizing factors by identifying cells that did not tolerate the treatment.
To fully leverage our high quality PRCISR™ CRISPR screening services, we provide extensive scientific support throughout the key aspects of your project.
Key Aspects:
PRCISRTM CRISPR bioinformatics
- Empirically validated CRISPRko gRNAs
- Sanity-checks on customer-provided gRNAs: on-target scoring, off-target identification, detection of undesired sequence patterns
- Selection of appropriate control sequences
- Barcoding
- Single cell RNA-seq compatibility
- Sequencing strategies for single, fixed-pair and dual-multiplex
- Sample demultiplexing and read counting
- Sequencing depth
- Data deconvolution with ReCo
- Replicate correlation
- Effect size determination
- Performance of control sequences
- Enrichment/depletion analysis (e.g. viability, FACS reporter)
- Combinatorial gene effects (e.g. genetic interactions, synthetic lethality)
- Pipeline of established tools: MAGeCK, PinAPL-py, BAGEL, drugZ, Gemini, …
- Custom pipelines
- Functional enrichment
- GO analysis
- Network biology
- And others
Vivlion offers bioinformatic support in the following areas:
- Library design: in silico design of gRNA sequences, sanity checks of customer-provided gRNA sequences (on-target scoring, off-target identification, detection of problematic sequences, identification/removal of duplicates), selection of control sequences, characterization of library pool (gRNA abundance and read counting, completeness, distribution skew)
- Data analytics: gRNA abundance and read counting, in silico quality control (enrichment and depletion of control gRNAs, gRNA, gene and phenotype correlation), single edit enrichment and depletion analysis with established and proprietary workflows, multiplex enrichment and depletion analyses, genetic interaction mapping, function and pathway enrichment analyses
- Optional: Single cell tracing by barcode assessments, data integration of prior knowledge and public resources (gene expression and function, protein-protein interaction, etc.)
Link to Paper ReCo: automated NGS read-counting of single and combinatorial CRISPR gRNAs
ReCo was developed as a stand-alone and user-friendly analytics tool for generating read-count tables of single and combinatorial CRISPR library and screen-based NGS data.
Wegner M, Kaulich M. ReCo: automated NGS read-counting of single and combinatorial CRISPR gRNAs. BioRxiv. Open the paper: doi: 10.1101/2023.03.09.530923
Contact us
We would like to hear more about your CRISPR questions and applications – please reach out to us by completing the following form:
