Demultiplexing service is included by default for all sequencing run types for standard barcodes. If you would like us to demultiplex, please provide barcodes in the libraries table in the COREOMICS submission system. Unfortunately, we cannot demultiplex inline barcodes.
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 "Label Density Calculator" program. "Bionano Access" also has such a feature. Both programs are available from this webpage: https://bionanogenomics.com/support/software-downloads/
The preferred label density for nickases is 8 to 15 labels per 100kb.
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 (following protocol instructions precisely). Other protocols can work too, but the spin column protocols are the most commonly used ones and very reliable.
Spin column DNA isolation kits are available from multiple vendors including Qiagen, Zymo, Omega Biotek, Sigma, and Norgen Biotek e.g.
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.
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 samples for both DNA and RNA
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 running one or more batches of RNA samples weekly on the high-throughput LabChip GX.
For UC Davis labs the cost per sample will be $5 (with a minimum of $10).
In order to generate usable data:
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 than recommended, you will generally run the risk of introducing biases and noise into your data.
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 requires additional handling and QC steps.
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.
