The Keck Facility

The Bay Paul Center is thrilled to welcome sequencing specialist Rianna Massoni to the Keck Facility. Rianna brings expertise in amplicon, genomic, metagenomic, and single-cell RNA sequencing, with a background in bioinformatics and machine learning. At the Darrin Freshwater Institute in Lake George, New York, her research explored how changes in aquatic environmental conditions affect microbial gene expression and community structure—experience that aligns with the interdisciplinary sequencing projects we support.

The W.M. Keck Ecological and Evolutionary Genetics Facility in the Josephine Bay Paul Center provides comprehensive Sanger and Illumina sequencing services, including project consultation, nucleic acid extraction, library construction, sequencing, and bioinformatic analysis to MBL resident scientists, courses, Whitman scientists, Grass Fellows, and the wider Woods Hole community.  Our core instruments include the ThermoFisher SeqStudio Flex for fast and reliable Sanger sequencing, and the new Illumina MiSeq i100+ for high-throughput amplicon, (meta)genomic, and RNASeq projects. Through the end of June 2026, members of the greater Woods Hole community (USGS, NOAA, WHOI, Woodwell, SEA) and UChicago can receive substantially discounted internal pricing on all Illumina sequencing services.

In addition, the Keck Facility offers access to resources for DNA and RNA manipulation and library preparation, including Gemini XPS and Promega GloMax plate readers, a Promega Maxwell nucleic acid purification platform, a Qubit fluorometer, a NanoDrop spectrophotometer, a Covaris S-220 ultrasonicator, a Sage Science BluePippin for DNA size selection, an Agilent TapeStation 4200 electrophoresis platform, and a ThermoFisher QuantStudio 5 Real-Time PCR System.  We also have stocks of AMPure XP clean-up beads and Illumina bar-coded primers.  There is no fee for trained Woods Hole personnel to use this equipment.  Cost of materials are listed below or bring your own.  For questions or training please contact keck@mbl.edu. Please enquire about additional charges for us to process your samples.

Sanger Sequencing

We employ an 8-capillary ThermoFisher SeqStudio Flex. We are retiring the Spectrum Compact CE System this summer. This 4-capillary sequencer was generously donated by the Promega Corporation to MBL's Education Department, in honor of service and contributions of Dave Remsen to marine biology. We accept purified PCR products or plasmid clones in single-tube, 8-strip, or 96-well format, and sequence using standard M13 primers or custom primers you provide. Use the link below to register your sequencing request. Please contact  keck@mbl.edu with any questions or to inquire about using the platform for fragment analysis or other applications.

Sanger Sequencing Request Form

Illumina Services

We now employ a MiSeq i100+. This latest instrument from Illumina has robust chemistry and greater flexibilty compared to our now-retired MiSeq and NextSeq 500. We thank Illumina’s customer service for helping us secure this new platform at considerable savings which we are passing on to users. The MiSeq i100+ is appropriate for most amplicon, (meta)genomic, (meta)transcriptomic, and RNASeq projects.  Through the end of June 2026 we are offering substantially discounted internal pricing to members of the greater Woods Hole community (USGS, NOAA, WHOI, Woodwell, SEA) and UChicago.

We can work with you at the any stage of the sequencing pipeline, including project planning, nucleic acid extraction, library construction, and sequencing, and we offer some bioinformatic support. We routinely provide service for mid- to high-throughput projects, and also accept small-scale projects to assess techniques or workflow. Please inquire about low-input or challenging samples, including single-cell or other custom libraries. Contact us at keck@mbl.edu to discuss your sequencing needs.

Illumina Sequencing Costs

Every project is unique. Samples may require DNA/RNA extraction, cDNA synthesis, or reconditioning (post-library low-cycle amplification for low biomass samples), and many libraries benefit from size selection. We also recommend and offer size selection and quantification on pooled libraries that you supply prior to sequencing. Examples of base prices for library construction, assuming we start with clean DNA or RNA, are:

Total sequencing costs of a project depend on the sample type and quality as well as the number of clusters, reads, or bases needed per sample. Please contact us at keck@mbl.edu for a detailed quote because every project is unique. Examples of pricing for standard projects are:

The table below summarizes Illumina expected number of clusters, number of reads (1x or 2x the number of clusters) and total bases sequenced (reads x read length) for different combinations of run type and flow cell type.  We generally exceed the number of clusters generated, and thus the yield of reads and bases > Q30.  Please enquire for details. 

Each cluster represents one DNA fragment from the original library