FAQs

Arbor will align your data to one reference genome (provided by you!), profile the CpG methylation status, and provide the output with summary statistics for the read QC and the read alignment QC. 

Arbor will perform read quality control and optional read pooling and perform de novo assembly with the industry-standard tool (Hifiasm). We can polish the assembly with short-read DNA sequencing data if desired. A summary of the assembly metrics and quality assessment will be provided along with the outputs. 

For de novo genome assembly, we provide contig-only assemblies. Raw methylation data will be delivered unless the methylation analysis bioinformatics package is also added to the project. 

Arbor will align your data to one reference genome (provided by you!), call variants with DeepVariant where possible or another variant caller where not possible and provide the output along with summary statistics for the read alignment and variant calling. This package includes calling single nucleotide polymorphisms and short INDELs. Structural variants are not included in this package. 

If you need a specific set of tools and/or parameters, we welcome custom bioinformatics projects. Customization of the pipelines and/or parameters is not included in our packaged offerings. 

We can accept a variety of samples such as cultured cells, bacterial, and various types of tissue from a wide range of organisms including plants, animals, and microbes. Please check our sample preparation guide for recommendations. If you don’t see your organism type, please contact us to discuss your project. 

Yes! If you would like to take full advantage of the capabilities of long-read sequencing, your starting material must be intact high molecular weight DNA. If your sample contains shorter fragments, you’ll sequence shorter-than-desired fragments. We require that you check the morphology and provide us with the image/trace as part of your sample submission.

We recommend sequencing with short-reads to ~30X coverage. We can generate this sequencing data for you or work with data you’ve already generated. 

It depends on your desired outcome. Minimally, we’d recommend 50M-100M reads. For more confident annotations, ~200M-400M reads. For performing high-quality annotations with multiple tissue, we’d recommend a total of 500M-1B reads, with each tissue type receiving ~50M-100M reads. 

We do not currently offer laboratory or analysis services for Hi-C data, but please contact us for a recommendation. 

We do not currently offer reference-grade quality de novo genome assembly services, but please contact us for a recommendation. 

Arbor will provide CCS reads that are demultiplexed, but otherwise raw in FASTQ and BAM format. 

You can order our SMRTbell® library preparation and Vega™ sequencing as a standalone service. We also have the flexibility to add high-molecular weight DNA extractions and/or bioinformatics analysis to either end of the workflow.

One! At minimum, you will need to order at least one SMRTbell® library preparation and at least one Vega™ SMRT® Cell. Beyond that, you can add as many or as few extras as your project requires. 

We are currently only offering full Vega SMRT Cell. You are welcome to split the Vega SMRT Cell across up to 384 samples. 

Protocol: myBaits Compass Kit v1.0 Manual

In the manual, you will find the complete protocol for kit use, as well as a detailed list of required supplies (reagents and equipment) that you will need in order to perform the captures.

Prior to executing the myBaits hybridization capture workflow, you will need to convert your DNA samples into next-generation (NGS) sequencing libraries with a compatible library preparation kit. Daicel Arbor offers the Library Preparation Kit for myBaits (sold separately) which is appropriate for creating NGS libraries from good quality or mildly degraded dsDNA samples prior to hybridization capture with myBaits. However for extremely degraded DNA samples, we recommend choosing a dedicated NGS library prep method that is intended for highly degraded and/or very low input dsDNA or ssDNA.

The myBaits Compass kit targets ~1.2M million SNP markers that are compatible with commonly used genealogical databases for FGG analysis. You can download the complete target sets here:

Compass target BED file, hg19 version (ZIP)

Compass target BED file, hg38 version (ZIP) 

Looking to outsource your research data generation? Our myReads NGS services laboratory team can provide DNA extraction, library preparation, myBaits capture, and/or short- or long-read sequencing from any sample type, even degraded DNA. Learn more on our NGS services webpage, or contact us for more info.

Please note that Daicel Arbor Biosciences’ products and laboratory services are provided for Research Use Only. Daicel Arbor Biosciences does not provide accredited forensics services.

The myTXTL Pro Kit is intended for cell-free protein expression of proteins that do not require disulfide bonds. It also has the highest yield of our two kits. The Antibody/DS Kit is intended for the expression of proteins that do contain disulfide bonds such as antibodies and enzymes. The yield of the Antibody/DS kit varies with the protein expressed, but for deGFP it is about 30-50% the yield of the Pro Kit. This is still enough protein for most downstream applications.

For work involving proteins that require disulfide bond formation we recommend our myTXTL Antibody/DS Kit. It is possible that some proteins with just 1 disulfide bond, such as VHH/Nanobodies, may express and show activity in the myTXTL Pro Kit, but generally speaking disulfide bond containing proteins will have the highest yields and best activity in the myTXTL Antibody/DS Kit.

If you were using any of our 3 original myTXTL kits, those will be discontinued in August 2024. The myTXTL Pro Kit is now the kit that will serve your needs as it has all the properties of the old kits combined into one: it supports linear and plasmid DNA as well as all E. coli promoters and also enables T7 promoter-based expression through the addition of the Pro Helper Plasmid that expresses the T7 RNA polymerase. It’s a comprehensive solution for cell-free protein expression. All Pro Kits include the Pro Helper Plasmid and a T7 deGFP Positive Control Plasmid.

If you are interested in expressing proteins that contain disulfide bonds, the myTXTL Antibody/DS Kit is what you need.

Yes, myTXTL reactions for cell-free protein expression have been conducted from 2 to 100 uL volume, but above 50 uL we recommend shaking and/or switching to a reaction vessel with higher surface:volume ratio to allow proper oxygenation of the reaction mix. myTXTL reactions are very sensitive to the amount of dissolved oxygen. If using over 50 uL volume, a flat-bottomed ELISA, deep well plate or tissue culture plate may be advised along with shaking at 650 RPM. We advise testing such a setup with one of the positive control plasmids, such as T7 deGFP. The key is to balance oxygenation and avoid the reactions drying out due to too much surface area. Please refer to the appropriate kit manual for additional guidance on scaling up reaction volume.

As the myTXTL platform relies on the endogenous transcription and translation machinery of E. coli, a functional gene cassette must contain a promoter that can be transcribed by E. coli RNA polymerase and associated transcription factors (primarily Sigma 70) or by a T7/T3 RNA polymerase if those polymerases are expressed from a helper plasmid (available in our Toolkit). The ribosomal binding site should also be compatible with E. coli translation machinery. For more general advice on how to construct a functional gene cassette, please refer to the current myTXTL handbook.

myTXTL supports all promoters used in E. coli protein expression, including promoters that rely on the endogenous E. coli transcription machinery and those that require a separate RNA polymerase such as T7. All kits come with a Helper plasmid to express the T7 RNA polymerase and enable transcription from T7 promoters. If a promoter is used that is recognized by the E. coli RNA polymerase, then this helper plasmid is not needed. If using a plasmid with an inducible promoter, such as the pET vectors, you need to add your inducer IPTG at 1 mM to the reaction and you may want to explore plasmid concentration in the range of y your inducer like IPTG if it is an inducible promoter.

All myTXTL kits support plasmid or linear DNA templates as well as mRNA.

myTXTL supports all promoters used in E. coli protein expression, including promoters that rely on the endogenous E. coli transcription machinery and those that require a separate RNA polymerase such as T7. Inducible plasmids require that the inducer be added to obtain the highest protein yield. pET (T7lac promoter) systems need 1 mM IPTG, for example, otherwise follow the guidance in the following table for inducer and plasmid concentrations in the myTXTL reaction.

We recommend the following inducer and plasmid concentrations when using some common inducible promoters: