When is a genome suitable for Bionano Optical Genome Mapping?

To check if the genome of your species of interest is suitable for Optical Genome Mapping on the Bioanao Saphyr, you should check the distribution of labeling sequence motifs. For this purpose, Bionano provides in silico digestion tools with the

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Which DNA isolation protocols do you recommend for Illumina sequencing?

We recommend DNA isolations with spin-column kits/protocols that should include an RNase digestion step. Spin column kits have the advantage that they will reliably generate clean DNA samples that are fully dissolved and have fragment sizes longer than 10 kb

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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

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What type of samples are recommended for RNA isolations for gene annotations?

What type of samples are recommended for RNA isolations for gene annotations? Please see the information on page three  of this PDF that we wrote originally for the California Conservation Genomics Program (CCGP). It contains recommendations for the collection of

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What type of samples are recommended for the isolation of HMW-DNA? (for Long-Read Sequencing)

What type of samples are recommended for the isolation of HMW-DNA? (for Long-Read Sequencing) Please see the information in this PDF that we wrote originally for the California Conservation Genomics Program (CCGP). It contains recommendations for the collection of samples

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How to submit samples for Labchip GX RNA-QC and fragment analysis?

Assessing the integrity of RNA samples with the Bioanalyzer can be time-consuming and expensive since each run takes an hour and only 12 RNA can samples can be run. To make RNA QC more convenient and affordable we will be

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Can I submit samples of lower integrity than recommended?

The sample integrity requirements are chosen to ensure the generation of high-quality data.  Please contact us before submitting such samples. It may be possible to use an alternative protocol that tolerates some sample degradation. When working with samples of lower integrity

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Can you run samples with less than the recommended input material?

The sample amount requirements are chosen to ensure both, high-quality data and efficient processing. Most of the library prep protocols will generate sequenceable libraries with lower input amounts than request, often requiring additional PCR cycles. Processing often low-input samples often

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How to purify DNA samples for long-read sequencing (PacBio, Nanopore)? How to remove polysaccharides?

DNA samples for long-read sequencing library preparations or also 10X genomics linked-reads have to be exceptionally pure. Please see the sample requirements.  For difficult DNA samples, especially all plant DNA samples with hard-to-remove contaminants (e.g. some polysaccharides), we recommend to carry out

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How to prepare samples for multiplexed amplicon sequencing on Illumina systems?

There are multiple valid protocols available for amplicon sequencing on Illumina systems.  Here we describe one of many options: A  two-step PCR protocol to generate complete sequencing libraries. This protocol has the advantage that it does not require custom sequencing primers

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