Frequently asked questions

Consult the list below to get answers to frequently asked questions about the Onyx Platform, Inscripta software, instrument, kits, assays, MAD7 nuclease, and other general questions.

Separator

Inscripta is selling the Onyx platform instead of offering a gene editing service because we believe our business model will provide more researchers greater access to CRISPR-based gene editing. The Onyx platform is easy to use so that any lab can use CRISPR-based gene editing to accelerate their microbiology-related research and development.

Inscripta will offer full product installation and ongoing warranty and service contract support through its Customer Success team (field service engineers, applications scientists, and technical support specialists).

Inscripta will offer both basic and expert product training. Basic training on the use of the instrument and Inscripta workflow will be provided to the customer at the time of installation of the instrument. Inscripta will also offer extended technical service and support for customers who need it.

Inscripta chemistry cannot be purchased separately, and the gRNAs must be purchased from Inscripta. The Onyx platform is designed to work together as a system to deliver optimal editing outcomes.

Purchase of the Onyx instrument and biological reagents from Inscripta for use in microbes (E. coli and S. cerevisiae) provides the user a license to the intellectual property owned by or exclusively licensed to Inscripta covering the Onyx instrument and biological reagents when used according to Inscripta’s terms and conditions. The customer will own all the data and output from the editing experiment, with no reach-through by Inscripta.

We will continue to release other species on the platform as and when the development and validation for a specific species are complete. Please contact us to let us know the species you’re interested in.

Yes, custom strains of E. coli and S. cerevisiae can be validated on the instrument using the Inscripta Customer Strain Validation Kit.

We currently support S288C from which BY4741 and BY4742 are derived. We anticipate that multiple derivative strains of S288C will be compatible with the platform. BY- and other S288C — derivative strains are on the short list of strains to support. Our platform enables the testing of custom strains using the Strain Assessment Kit, after which the Inscripta editing pipeline can be executed.

In essential genes, we likely will be unable to make knockouts, but we should be able to make a high percentage of site-saturation and other design types. Edit rates can be influenced by a few factors, including gRNA, HDR efficiency, and genomic context. Payload size negatively impacts edit efficiency, meaning that a larger payload size has lower editing efficiency than a smaller payload size. The impact of payload size also depends on the edit type. Impact by edit type follows this order: insertion > swap > deletion, meaning that large insertions have much lower editing efficiency as compared to large deletions. Target regions that are difficult to edit are those containing repetitive elements and extreme GC content (e.g. <25% or >70% GC).

The Onyx platform manages the complexities of cell management and transformation efficiency, allowing biologists to concentrate on the outcome of the editing experiment. We optimize the growth, transformation and other steps in the editing process such that our output cell libraries have adequate representation of each edit cell type. At the end of the editing experiment, we will provide metrics associated with library coverage, library editing and coverage per design.

No. The Onyx instrument can execute a protocol to make electrocompetent S. cerevisiae or E. coli cells through an automated workflow that ensures consistency from experiment to experiment. The workflow starts with ~10e7 cells in 50 µL glycerol stocks.

Inscripta scientists have optimized transformation protocols for E. coli and S. cerevisiae that are automation-friendly, using a combination of standard and custom techniques/​adaptations to obtain reproducible transformation. Details of the transformation protocols are proprietary.

The file format is CSV. At some point in the future, we also will support JSON.

Uploading the full genome of your custom strain is the best way to ensure the creation of robust custom gene editing reagents for your editing experiment. While we can work with partial genomes in special cases, there are trade-offs with respect to ensuring robust performance due to the subtle but significant variations between genomes reported in the public database and the actual genome of the custom strain.

YTTN for E. coli and TTTN for S. cerevisiae. InscriptaDesigner software is capable of aiding researchers in designing edits using these sequence motifs.

~90% of positions in the MG1655 genome are within 20 NT of a YTTN PAM. We have designed genome-wide promoter insertion libraries covering >98.6% of CDS regions in the E. coli genome. Edit rates can be influenced by a few factors including guide and HDR efficiency and genomic context.

~90% of positions in the S288C genome are within 20 NT of a TTTN PAM. We have designed genome-wide knock-out libraries covering >98.5% of CDS regions in the S. cerevisiae genome. Edit rates can be influenced by a few factors including guide and HDR efficiency and genomic context.

The Onyx instrument is an essential part of the platform, which consists of our software, instrument, consumables, and assays. They are optimized to work as a package to deliver superior results, exceptional editing efficiency and design library coverage. The Onyx instrument manages your cell population optimally for each run. Control and efficiency are required during and between each operation of the genome engineering process and are key for successful massively parallel precision editing. Optimized instrument protocols that employ dynamic feedback ensure performance reproducibility, saving you time and eliminating costly errors. In our lab of highly trained synthetic biologists, we have observed that manual, benchtop genome editing is variable, slow, and labor intensive. In contrast, our technology enables genome engineering on a massive scale.

In contrast to currently available options for microbial gene editing that rely on either manual workflows or plate-based, large-scale automation, Onyx enables automated gene editing in a benchtop instrument at the push of a button, utilizing several patented microfluidics that precisely manages time and temperature, monitors cell growth, and controls for the non-linearities of biological processes during the editing process. These microfluidic devices in Onyx execute key gene editing steps that include cell growth, electrocompetency, electroporation, cell recovery and cell editing and outgrowth.

We expect the same instrument to be used in the future for other microbial strains and species, with additional modules, features or workflows enabled.

The Onyx Platform will deliver one library at the end of a run, with up to 10,000 edits per library in E. coli and up to 6,000 edits per library in S. cerevisiae.

No. Transformation and liquid handling are only two of the many functions the instrument performs during an editing experiment. The instrument grows cells, makes them electrocompetent, transforms cells, and manages growth and recovery via customized microfluidics, liquid handling, digital partitioning and culture of cells.

Yes, the instrument needs to be connected to the Internet to operate and to complete the process of validation on the Inscripta Portal before a run can be initiated.

Approximate dimensions are 29” W x 25” H x 22” deep or 73 cm W x 63 cm H x 54 cm deep. The weight is 229 lbs or 104 kg. Yes, it will fit on a standard benchtop.

The instrument requires one 120 Volt AC, 15A circuit to provide power. Internet access is required to run the instrument.

The instrument can be cleaned by wipe-down with 10% bleach solution. The system is also equipped with a UV light source for internal deck/​cabinet sterilization between runs.

The instrument will need special handling during installation, which will be taken care of by the Inscripta field service engineer (FSE). The glass is tempered but it is not shatterproof.

Run time is approximately 2 days for E. coli and between 3 and 4 days for S. cerevisiae (Inscripta strains).

Inscripta genome engineering kits will include all the required consumables, from glycerol stock cells to an edited cell library. 

Custom gene editing reagents will be delivered to the customer within 3 weeks in North America (+1 week in Europe due to import/​export logistics) after the design order is submitted. An Inscripta Account Executive will update the customer about the expected delivery timelines.

Our manufacturing process is proprietary and includes various optimized reagent manufacturing steps to ensure efficient delivery of edited libraries.

At present, our software, consumables and edit performance have been optimized for the MAD7 nuclease.

MAD7 editing performance is comparable to Cas9 but utilizes different PAM recognition sequences. MAD7 is a staggered-end cutter rather than a blunt-end cutter.

We have tested multiple edit types genome-wide including gene knockouts, terminators, insertions and protein saturation mutagenesis. We have seen average edit rates of 30%. We are very stringent in our definition of an edit.” Only edits that are precise (complete and intended) are considered in our edit rate calculation.

Targeting of unintended loci can result from many factors, including gRNA design, the host cell’s ability to repair cut dsDNA, and the host genome. We are in the process of evaluating MAD7 specificity in many organisms, including mammalian systems. There are a range of published methods for assessing and controlling off-targeting.

We have a library of other MADzymes and enhanced MADzyme variants with substantially altered PAM preferences and other biochemical characteristics for different experimental needs. Please contact our Business Development team to schedule a further discussion with the Inscripta Enzyme Engineering team.

The short answer is: yes. Please contact our Business Development team to schedule a further discussion with the Inscripta Enzyme Engineering team.

The MAD7 variant supported on the platform is identical to the one released publicly on our website, which is a codon-optimized nuclease from the Eubacterium rectale genome (refseq WP_055225123.1). The codon optimized nuclease is 76% identical to the native Eubacterium rectale nucleotide sequence.

Yes. MAD7 has been tested in vitro and works comparably to other nucleases.

No. If you are interested in getting access to dMAD7, please contact our Business Development team for further discussion.

The MAD7 nuclease belongs to the Cas12a family and is a remote homolog of Cpf1. It shares about 25% identity to Cpf1.