DNA extraction service at Uppsala Genome Center
The success of any long-read sequencing project will depend mainly on the integrity and purity of the input DNA, which again can depend on storage and handling of both starting material and the extracted DNA. At Uppsala Genome Center, we have been working with High Molecular Weight (HMW) DNA extractions since 2016, and gained experience with extractions from many different organisms using commercially available HMW DNA extraction kits and traditional methods, as well as in-house developed workflows.
Uppsala Genome Center now offers HMW DNA extraction as a service for sequencing projects at or in collaboration with NGI and SciLifeLab. At this page, we describe shortly a number of extraction methods that we have evaluated in our lab.
Please note that we can not work with samples that are potentially infectious to humans.
For a more comprehensive description of extraction methods, please consult Appendix D - extraction material guidelines (pdf).
Currently first choice extraction method at NGI-UGC unless circumstances dictate otherwise. In our experience, Nanobind kits provide superior recovery, length and purity of DNA compared to other kits. Circulomics Nanobind protocols for different sample types can be found at the Circulomics online store.
In situ agarose plug extraction is especially suited for Bionano optical mapping and samples requiring shipping as the agarose protects the DNA from fragmentation. It is not recommended for applications that do not require ultra HMW DNA as the viscosity and potential agarose remnants can interfere with library preparation and sequencing. Bionano's protocols for agarose plug extractions can be found at Bionano's website.
HMW DNA purification on a dialysis membrane
Agarose embedded bird's blood
Plant wash buffer gradient, in different stages of purification.
SDS/CTAB lysis and phenol-chloroform extraction
Recommended for samples displaying purity issues when using other extraction methods. Especially useful for samples high in polysaccharides, phenols, fats and/or pigments. For this type of extraction, UGC tailors the workflow to each specific sample.
Only recommended by NGI-UGC for samples expected to be low in contaminants (such as vertebrate blood and tissue). This is a less expensive option and can provide 100 - 200 kb fragments from high quality material. The MagAttract protocol can be found in QIAGENS's webshop.
HMW-DNA extractions can be very laborious. We are therefore unable to process a large number of samples simultaneously.