Microbiome Core Facility Services

We aim to provide a collaborative atmosphere that is engaged in providing microbiome services that begin at the onset of the experimental design through data interpretation of the results obtained from various microbial assays. We have well established protocols for DNA exractions from diverse sample types and workflows for 16S and 18S analysis. All procedures are performed in dedicated hoods to minimize the possibility of background or cross contamination during sample processing.



Project management

  • SOPs for all processes
  • study design
  • sample tracking

Aliquoting samples (fecal, oral)

  • aliquot frozen aliquots into cryovials
  • maintain, organize and QC inventory of samples for project

Nucleic Acid extraction

  • Qiagen DNA kits (Powersoil Pro)
  • Qiacube HT automated extraction

Sample Quality Assessment and Shearing

  • Qubit
  • Agilent Bioanalyzer 2100 assays
  • Nanodrop

Microbiome Profiling

NanoString Assays


Agilent Bioanalyzer

Agilent Bioanalyzer

The Agilent Bioanalyzer DNA assay leverages microfluidics technology, enabling the quality analysis of DNA using only 1ul of sample. The assay is run on the Agilent 2100 Bioanalyzer instrument and utilizes the Agilent 2100 Expert Software to analyze and display results. RNA and DNA fragment sizes and concentrations are generated for each sample.

Assay types and information:

Qubit Fluorometer

Qubit Fluorometer

The Qubit 2.0 Fluorometer quantitates DNA, RNA, and protein with unprecedented accuracy, sensitivity, and simplicity. It is designed for molecular biology labs that work with precious samples that are rare or difficult to process and applications requiring precise measurement, such as real-time PCR.

Qubit vs NanoDrop

Assay Type Size Range Concentration Range Max # of samples per chip
Bioanalyzer DNA 1000 25 - 1000 bp 0.05 - 50 ng/ul 12
Bioanalyzer High Sensitivity DNA 50 - 7000 bp 0.005 - 0.5 ng/ul 11
Qubit dsDNA BR any 0.1 - 1000 ng/ul NA

Promega Glomax Discover

Promega Glomax Discover 

The referenced media source is missing and needs to be re-embedded.

Promega GloMax® Discover is a ready-to-use multimode plate reader developed with Promega reagent chemistries to provide a simple means of detecting luminescence, fluorescence and absorbance. This advanced plate reader provides flexible use of filters and includes high-performance luminescence, fluorescence, UV-Visible absorbance, BRET and FRET, two-color filtered luminescence and kinetic measurement capabilities.

S220 Focused-ultrasonicator

The S220 Focused-ultrasonicator is a versatile, high power system engineered for pre-analytical sample processing with Covaris’ patented Adaptive Focused Acoustics™ (AFA). Utilizing a spherical acoustic transducer, specifically designed AFA Tubes, and advanced electronics, AFA delivers controlled energy precisely and accurately to sample volumes from 25 μl to 10 ml.

The versatility of the S220 Focused-ultrasonicator makes it possible to bring the advantages of AFA to numerous biological and chemical applications, including DNA, RNA, chromatin shearing, tissue homogenization, cell lysis, compound dissolution and particle micronization.

The S220 Focused-ultrasonicator is computer controlled by SonoLab™ Software that incorporates preset protocols for standard methods, such as DNA shearing to specific fragment lengths, and easy-to-use-tools for user-defined protocols. The S220 is also compatible with ActiveX control if required for more specialized customer-defined, laboratory automation applications.

Advantages of DNA shearing with Covaris:

  • Reproducible, narrow size distribution
  • Non-contact, closed tube–no chance of cross contamination
  • Isothermal, high recovery process
  • Compatible & validated with ALL Next-gen sequencing platforms—SOLiD/Ion Torrent, Roche/454, Illumina/HiSeq to MiSeq

Submission Request for Covaris Shearing U

  • Email microbiomesr@duke.edu to request submission information.
  • It is required to provide a Covaris Shearing protocol and desired fragment length (bp) when submitting samples.

START: Shearing with Covaris S220 Focused-Ultrasonicator 

Sample Requirements, Tubes and Protocols 

  • 1.5-3 ug of genomic DNA or as directed by the library prep protocol in 1.5mL tubes
  • 50 ul or 130 ul for the microTube (for shearing sizes between 150 - 1500 base pairs)
  • 200 ul for microTube (for shearing sizes between 2000 - 5000 base pairs)
  • 1,000 ul for the milliTube

Step 1: Schedule a consultation with us by emailing us at microbiomesr@duke.edu prior to experiment and sample submission.  We will also include a NanoString representative if needed for the consultation.

Step 2: Review publications that have utilized the NanoString technology.

Step 3: Select from predesigned panels or design your own panel. Contact support@nanostring.com for NanoString panel information. For technical support contact jmadrigal@nanostring.com

Step 4: Refer to the table for information on the sample requirements and preparation guide.

Step 5: Submit service request and sample information via our online submission form. Sample requirements depend on sample type and panel, contact us at microbiomesr@duke.edu for details.

Step 6: Submit samples to the core at MSRB3 at prearranged time.

Data Analysis and Computational Resources: 

Data Management:

Data will be returned to the investigator by SFTP (NGS results) or through DukeBox (all other data). Instructions will be sent to investigator on how to download the data once results are posted.