DNA Strand

The GRT Hub offers optical mapping services using the Bionano Saphyr 2 instrument. The Saphyr instrument images High Molecular Weight genomic DNA (HMW gDNA) molecules that have been labeled at specific sequence motifs. These images can then be used to create a hybrid scaffold combining optical mapping data with Next Generation Sequencing data forming longer contigs. For more information please visit Bionano's guide on How Optical Genome Mapping Works.

Planning Your Experiment

Extraction of HMW gDNA is necessary for generating ultra-long DNA molecules for optical mapping. Bionano Genomics has validated protocols on their website for a variety of organisms as a resource. The HMW gDNA is labeled using fluorescence at sequence specific motifs.  Bionano recommends a label density between 9 to 25 labels per 100kbp. Label density for your genome can be calculated using Bionano’s Label Density Calculator.

The following are links to some Bionano guides that may be helpful when planning your experiment:

Bionano Sample Preparation/Storage/Shipping Recommendations

Samples can be submitted to GRT Hub as tissue samples, extracted HMW gDNA or biological material embedded in agarose plugs. To keep the samples in pristine condition, please follow Bionano Genomics’ recommended shipping protocols:

For more information, please see the Bionano Genomics Website.