How should I QC my genomic DNA samples before sequencing?

DNA Sample Integrity:

For Illumina short-read sequencing:
DNA sample integrity should best be QC-ed by agarose gel-electrophoresis and ethidium bromide staining. “Safe” gel-stains such as Gel-Red work just as well.
These stains will make both DNA and RNA visible. RNA will run as an halo-like smear in the range 50 to 300 bp.
We suggest a 1% agarose gel and a ladder marker that best includes a 20 kb band like the GeneRuler 1kb Plus DNA ladder from Thermo Scientific. Please load about 40 to 100 ng DNA for each sample. Other conditions can work as well.

The agarose gel image will show the presence or absence of RNA contamination and provide the best information on potential sample degradation.
Please email us an agarose-gel image before shipping the samples in case of any concerns. Please always ship a copy of the agarose-gel image together with the samples.

For PacBio or Nanopore long-read sequencing:
HMW-DNA samples should be QC-ed via pulsed-field gel electrophoresis (PFGE) or field-inversion gel electrophoresis (FIGE). We can carry out this QC for you. The Femto-Pulse will instrument enables capillary FIGE with ultra-low input amounts and will provide a digitized data analysis (similar to the Bioanalyzer for short molecules).
If you do not have access to these technologies, we suggest running a longer conventional agarose gel (as described above) to get a first idea about the sample quality before shipping the samples to us for a FIGE analysis.

Please always ship a copy of agarose-gel images together with the samples.

DNA Sample Purity:

DNA sample purity has to be determined via spectrometry. Please see the sample requirements page for the recommended values for your protocol. It is certainly helpful to also record the entire UV absorption spectrum as it provides additional information. For DNA samples the 260/230nm ratio should be >2 and the 260/280nm ratio 1.8-2.0 .

 

Please also see:

Which DNA isolation protocols do you recommend for Illumina sequencing?

How should I purify my samples? How should I remove DNA or RNA contamination?

Do you offer DNA isolations and RNA isolations as a service?

How do I prepare DNA samples for RR-Seq (reduced representation sequencing)?

 


Category: 03 Sample Preparation & Sample Requirements

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