FAQs

• Decreased sequencing turnaround time. With the sequencer in Arbor’s hands, we’re in full control of the speed and can provide data at least 2 weeks faster than ever before.
• Increased read quality. Runs frequently produce results with >90% of reads meeting or exceeding Q30 quality scores. 
• Flexibility. Mid-sized flowcells (~240Gbp) make flowcell-level pricing accessible for smaller project sizes.
• Compatibility. The AVITI is compatible with all of Arbor’s existing short-read library preparation (and capture) options, so you can feel confident knowing that your precious samples will be handled with the protocols you trust. 

While the output (FASTQ files) is the same, the sequencing chemistry is different. The AVITI uses “avidity sequencing,” which is a sequencing-by binding chemistry. Illumina sequencing employs a sequencing-by synthesis chemistry. The avidity sequencing chemistry improves the accuracy of the basecalls. Read more about avidity sequencing here.

AVITI is the new short-read medium-throughput sequencing platform from Element Biosciences. It is a drop-in replacement for Illumina sequencers – meaning that it is compatible with Illumina libraries and the data format is the same as you’d get with an Illumina sequencer.

Many sample types and species will require special permits for shipping internationally (or domestically). We can provide some advice, but ultimately you are responsible for proactively identifying the permit(s) that are required for your unique samples. Some examples of biological samples that require permits are tissue or DNA from CITES-listed specimens and plant tissues regulated by the USDA/APHIS.

If Daicel Arbor Biosciences is required to apply for an import permit on your behalf, you will be required to pay a permit application fee, regardless of whether the application is successful.

We strongly encourage our customers to research shipping regulations before contacting us about your project to determine your specific permit needs. Incorrect or incomplete documentation may result in the seizure and loss of your samples at Customs, and potentially the assignment of fines/fees.

Yes. We require documentation that all relevant and necessary ethics approvals have been granted for any human specimens that you would like us to work on. This includes both contemporary and ancient samples and includes both tissue and nucleic acid derivatives. Please contact us to receive our Ethics Statement document if you are interested in sending human samples to us. We do not accept clinical specimens and are not CLIA-certified.

We prepare short-insert libraries with 8-bp unique dual indexes.

We prepare long-insert libraries with 16 bp identical dual indexes.

Our library preparation protocols have been carefully tested and optimized for both WGS and targeted sequencing applications. We have protocols that are appropriate for a wide range and variety of input qualities and quantities that have been successfully applied to thousands of samples. Therefore it is very likely that one of our existing protocols will work well for your application, but if you have very specific project constraints, our NGS experts would be happy to discuss the options with you.

Upon arrival, we will take a look at your shipment and plastics to ensure that the samples have not been damaged during their journey. At that point, your project will enter our QC queue.

For Standard and Long Insert quality DNA samples, we will quantify the total gDNA with a spectrofluorometric assay, purify up to 80% of the material, and re-quantify the samples. For Degraded quality DNA samples, we will perform the initial total gDNA quantification as well as visualize at minimum a subset of your samples on the Agilent TapeStation platform. For Ancient quality DNA samples, we will perform the initial total gDNA quantification and may visualize a subset of your samples on the Agilent TapeStation platform.

For RNA samples, we will perform a total RNA quantification. If you have ordered our RNA clean-up, we will perform a DNase treatment, a bead-based purification, a visualization via Agilent TapeStation, and a second total RNA quantification.

For pre-made libraries, we will perform a total gDNA quantification as well as a qPCR-based assay for properly adapted Illumina-compatible library molecules.

If you order QC-only services, the “Standard QC” is the same as the Standard DNA quality QC above. The “Extended QC” is the same as the Degraded DNA quality QC.

We will provide a QC report with the results of our QC to you when you send us DNA, RNA, or libraries. We will also perform the appropriate QC and send the QC report for samples for which we perform the DNA/RNA extraction.

Yes. You can order our “Degraded DNA Package” if you would like our full service package or “Extended QC” if you would like a custom project configuration and we will evaluate the quantity and the quality of your samples. You will be provided with a QC report and our NGS experts are available to consult with you about the results and can suggest some options for moving forward with your project.

Yes. We are able to expedite a select number of projects at a given time. Please inquire if you believe your project needs to be expedited and we will let you know if we have availability in our expedited pipeline and if the desired project timeline is feasible. When a project is expedited, it will skip our regular queue. We do not guarantee a specific turnaround time guarantee for expedited projects. We will do our best to be transparent with anticipated timelines and will communicate progress as well as delays with you during the process.

Yes. Please do your best to provide your project information as accurately as possible and we would be happy to provide a price estimate for you to use in your grant proposal. However, please be aware that our prices may change between when your estimate is provided and when your grant is funded.

We pride ourselves on our professionalism, which goes beyond technical expertise. We have a team of highly skilled bioinformatics experts with years of experience in NGS data analysis, ensuring the accuracy and reliability of your results and we emphasize clear and regular communication, proper planning, and execution to ensure the best possible collaboration and experience for our clients. We offer a comprehensive suite of bioinformatics services and strive to be flexible by providing personalized service tailored to your specific needs and preference. We use state-of-the-art software and computing resources to ensure that your NGS data is processed quickly and accurately. Additionally, our commitment to excellent customer service and support is unwavering throughout the entire process. We are always available to answer questions, provide guidance, and work closely with our clients to ensure the success of their projects.

The pricing of our bioinformatics services depends on the specific requirements of your project. Once you contact us, we will provide no-charge project consultation upfront to assess your needs and determine a detailed project plan, after which we can quickly provide you with a detailed quote.

The custom bioinformatics service process begins with a consultation to understand your research goals and project requirements. Our team of experts then provides tailored solutions, including customized data analysis pipelines, software development, and consulting services, to meet your specific needs. The final results are delivered in a timely and reliable manner, providing you with actionable insights to support your research.

The timeline for results will depend on the complexity and scale of the project. As our clients often work under tight timelines, we are adept at expediting processes in the most efficient manner possible. Our team of experts will work with you to establish a timeline that meets your needs and ensures timely delivery of results.

Our team of experts uses state-of-the-art algorithms and computational methods to deliver high-quality, reliable results. During our upfront consultation, our goal is to find the most appropriate pipeline match for your research goals and project configuration. We perform quality control checks and validation throughout the bioinformatics analysis process to ensure that our results are accurate and trustworthy. We are available for support and consultation prior to, during, and after a project to answer any technical questions.

Our standard deliverable consists of a comprehensive project report that outlines our methodology, workflow, tables, and figures. We can also tailor our deliverables to your preferences, such as intermediate files, customizing figures and tables.

Likely yes. Our team of scientists at Daicel Arbor Biosciences come from a range of scientific backgrounds and possess expertise in diverse applications, data analysis workflows and bioinformatics tools. It is likely that our team members have experience working with datasets and analyses that are comparable to yours, and they have a proven track record of effectively handling projects applicable to a diverse range of research fields, such as agrigenomics, non-model organism genomics, functional genomics, phylogenetics/phylogenomics, genotyping, degraded or ancient DNA, and more.

No, you do not need to have any bioinformatics expertise to work with us. We will have a consultation to understand your requirements and plan the project accordingly. Your final project report will include comprehensive methodological descriptions in sufficient detail to populate the methods section of a peer-reviewed publication.

By default, we provide a storage term of three months for project deliverables. However, we do offer the option of longer-term storage upon request, subject to an additional fee.

A standard protocol for chemical transformation usually produces E. coli cells with a sufficient competency for plasmid intake. We recommend following the procedure described in Sambrook et al. 1989.

Several factors can hinder protein synthesis in the myTXTL cell-free protein expression system, including:

1. Master mix inactivation due to improper storage. The myTXTL master mix must be stored at -80°C and number of freeze-thaw cycles should be minimized.
2. Improper reaction setup, Please review the recommendations to set up a myTXTL reaction in the current myTXTL manual.
3. Contamination of myTXTL reaction with nuclease. To avoid nuclease contamination, wear gloves and use nuclease-free water, sterilized tips and tubes. Use deionized, nuclease-free, “molecular grade” water for myTXTL reaction setup.

Batch-to-batch variation can cause varying levels of TXTL inhibitor contamination present in the plasmid solution. Please follow our recommendations on how to prepare template plasmid DNA for TXTL reactions in the current myTXTL manual.

If you have started your project with plasmid templates for which you purchased the myTXTL Sigma 70 Master Mix, but now you want to try out linear DNA templates with the myTXTL Sigma 70 Master Mix you still have available in your lab. A simple addition of myTXTL GamS Protein to the myTXTL Sigma 70 Master Mix significantly boosts protein output from linear DNA templates in this master mix. For future work with linear DNA templates we would recommend the myTXTL Linear DNA Expression kit or myTXTL T7 Expression kit as both use the myTXTL Linear DNA Master Mix.

The kit used depends on the phage’s genome type, if it is linear DNA, we recommend the myTXTL Linear DNA kit or myTXTL T7 Expression Kit if you need to express accessory proteins. If circular DNA or RNA, any of our kits could be used, keeping in mind that non-E. coli phages may require the addition of their host’s primary transcription factor (SigA/Sigma70) or other accessory proteins to enable replication (see Emslander et al. 2022).