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.

START: Microbiome Services: Sample Submission Request

Project management

  • Sample collection kits
    Custom kits
    DNA genotek
  • SOPs for all processes
  • REDCap support for microbial studies

Aliquoting fecal samples

  • Frozen fecal aliquots into cyrovials

Nucleic Acid extraction

  • Qiagen DNA kits

Sample Quality Assessment and Shearing

  • Qubit
  • Agilent Bioanalyzer 2100 assays
  • Covaris Shearing

Microbiome Profiling

NanoString Assays

*Coming soon: Anaerobic Coy Chamber access

Agilent Bioanalyzer

gloved hand and emptying pipette into 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
DNA 1000 25 - 1000 bp 0.05 - 50 ng/ul 12
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

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.

Covaris instrument

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

Service Pricing and Summary 

Contact us at microbiomesr@duke.edu for Covaris service pricing.

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
NanoString instrument

Step 1: Schedule a consultation with us by emailing us at microbiomesr@duke.edu or calling 919-668-1583 prior to experiment and sample submission.  We will also include a NanoString representative if needed as well in the consultation.

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

Step 3: Select your gene panel from a predesigned panel or design your own panel. Contact Greg Bauer at gbauer@nanostring.com for NanoString panel and Master Mix pricing and custom panel information. For technical support contact Tadas Rimkus at trimkus@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 Monday and Tuesday between 2 - 3 p.m. outside the entrance of MSRB3. Contact us to schedule another time if needed. 

Data Analysis and Computational Resources: 

Data Management:

Data will be returned to the investigator via Duke Data Service. Instructions will be sent to investigator on how to download the data once results are posted.