Genomics Core

Some DNA extractions are suitable for automation and some are better suited for manual extraction. Automated extractions are performed on a KingFisher Flex using Zymo Research kits and manual extractions are performed using Qiagen extraction kits.  Please contact Core Facility staff to discuss which method is best for your sample type.

Genome and metagenome libraries are prepared using Illumina’s DNA Prep kit (formerly Nextera DNA Flex Library Prep). The starting material needed is 50-250 ng of DNA in less than 15 uL volume, diluted in Tris-HCl, pH 8. The DNA should have an absorbance of 260/280 in the 1.8-2 range and 260-230 in the 2-2.2 range. Contact Core Facility staff if your template DNA does not meet these specifications. 

The costs below are for library construction of extracted, quantified DNA.  Next you will need to select the appropriate MiSeq or NovaSeq run.

Amplicon libraries are prepared with Illumina’s two-step PCR Nextera XT amplicon protocol.  Users can prepare their own PCR products or Core staff can fully prepare the amplicon libraries with common primers for 16S, ITS, and COI.  Please contact Core staff prior to preparing your own library to confirm compatibility with Illumina sequencing platforms, as specific adapters are required.  These are the costs for library construction of extracted, quantified DNA.  For full library prep, DNA should be diluted to 10 ng/ul, with 10 ul provided.  Next you will need to select the appropriate MiSeq or NovaSeq run.

RNA libraries are prepared using Zymo Research’s Zymo-Seq RiboFree Total RNA Library Kit, which can include an rRNA depletion step.  The minimum input amount of RNA is 100 ng, but the recommended input is 500 ng.  RNA should have A260/A280 and A260/A230 ratios >1.8 and be DNA-free.  Please check that this kit is compatible with your needs. 

The costs below are for library construction of extracted, quantified and quality confirmed RNA.  Next you will need to select the appropriate MiSeq or NovaSeq run.

The Illumina MiSeq is a benchtop sequencer specialized for lower-output runs on single-lane flow cells, offering Illumina’s longest read length of up to 300 nucleotides, paired-end. The MiSeq is ideal for amplicon sequencing, such as for bacterial 16S rRNA, and small genomes.  It can also be used to test larger runs prior to running them on the larger Illumina NovaSeq. 

The appropriate Illumina MiSeq flow cell for your project is determined by the depth of coverage needed, as well as the desired read length.  Contact Core facility staff for advice on which flow cell is right for your project. The costs below are for a PREPARED library.  Costs for library prep done at the Core facility listed on this website are in addition to the cost of the flow cell.

The NovaSeq 6000 is a large-scale sequencer from Illumina, generating unprecedented output in less than two days using patterned flow cell technology, with scalable through-puts to accommodate most projects. Careful consideration of sample numbers and flow cell output is crucial for effective use of this platform. The high yields of the NovaSeq flow cells may present difficulties in efficiently filling flow cells for many researchers.  As such, we offer some flow cells by individual lanes to reduce costs for users.

The appropriate Illumina NovaSeq flow cell for your project is determined by the depth of coverage needed, as well as the desired read length. Contact Core facility staff for advice on which flow cell is right for your project. The costs below are for a PREPARED library.  Costs for library prep done at the Core facility listed on this website are in addition to the cost of the flow cell.

For assistance calculating coverage necessary for your specific project, visit Illumina’s Coverage Calculator.