Table of Contents

Project specifications

The first and most important part of the submission process is to determine what YOU want from the project! There are several important considerations that will impact the overall quality of the resulting assembly and the venues for its dissemination. Here are some important questions to consider:

  • **Do you want this to be the reference genome for your species? **

While we already have a high quality reference genome for cattle, we are actively seeking samples to create references for other bovid species. If your species has not already been sequenced and assembled, your sample may make a fantastic reference assembly! If so, we strongly recommend that you consider using our trio-binning method and that you cross your target species with a compatible bovid species. You will then need to sequence the parents and offspring F1 with Illumina short-reads and prepare a sample from the F1 to send to us for long-read sequencing. We also highly recommend the generation of Hi-C data for assembly validation and scaffolding. Unfortunately, we are unable to provide Illumina or Hi-C data for your project, but we highly recommend this data to improve the quality of your reference.

  • Can you cross this breed/species with another to generate hybrid, F1 offspring?

If you are able to cross your breed with another, we highly recommend this over other project designs. Additionally, we highly recommend the collection of tissue samples other than blood, liver or semen from the hybrid offspring. The reason for the former recommendation is that your sample will be suitable for our trio-binning method, which results in the highest quality and most continuous assemblies. The later recommendation will ensure that your input DNA will be the highest quality for sequencing, and will allow us to assemble immune gene loci (which are difficult to assemble in blood samples). We understand that not all projects are able to accommodate this request; however, this does result in the best end assemblies.

  • **Can you only submit previously collected samples? **

In some cases, you may only be able to send tissues or DNA that have been already collected. We understand that many samples from heritage breeds or from ongoing research projects may be precious commodities, so we are still happy to work with you to identify if your samples are suitable for BPC sequencing. Please make sure that your samples conform to all of our following guidelines for sample submission. Also, please ensure that any sample you submit is replaceable or replenishable! We may use all of the sample in our sequencing library preparations and may not be able to return remnants for your future projects.

Sample quality guidelines

Not all labs have the same quality control equipment. We will specify the minimal metadata/QC requirements for sample submission for BPC projects, and then specify recommended metadata entries. Projects that conform to recommended specifications will be preferentially sequenced first, mostly due to the convenience of having more accurate data on the specimen! Sample submissions without all of the minimal metadata will not be sequenced until more information is provided by the submitter.

  • Minimal, metadata/QC requirements
    • Origin tissues
      • Not semen or liver
    • Metadata
      • A picture of the individual/breed
      • A completed metadata information sheet (coming soon!) on the sample
    • DNA UV/Vis absorbence spectra
      • Close to 1.8 260/280 ratio (+/- 0.1 range)
      • Close to 2.1 260/230 ratio (+/- 0.2 range)
    • Molecular weight metrics
      • Agarose gel images with high molecular weight ladders (top band > 30 kb)
      • Smeared DNA preps may not be acceptable for sequencing
    • Concentration
      • 50-200 nanograms per microliter
      • greater than 10 micrograms total mass
  • Recommended, metadata/QC requirements
    • Origin tissues
      • Lung or muscle
    • Molecular weight metrics
      • Fragment analyzer or Bioanalyzer plots
      • Average DNA molecule size is estimated to be greater than 100 kb
    • Concentration
      • 200 nanograms per microliter
      • 10 to 30 micrograms total mass

Sample submission process

Coming soon!