Quality Control and Support Instrumentation

Sample Preparation

NanoDrop 1000​NanoDrop 1000

The NanoDrop 1000 spectrophotometer is available on a first come, first-served basis, free of charge. Users are asked to supply their own tips, gloves, P2 or P10 pipettor and appropriate solution for blanking.

Uses 2 ul of nucleic acid or protein sample.

No dilution is normally required.

No cuvettes required.

Dynamic range of 2 to 3,700 ng/ul ds DNA

Measures absorbance in ultraviolet (UV) and visible light ranges.

Please request training if you are a first time user or need a refresher on how to use the instrument.


Covaris Sonicator​Covaris Sonicator

The Genomics Division houses Covaris Sonicator instruments that are used to prepare sheared or fragmented nucleic acid, proteins and tissues. The Covaris S2 system is a single-cuvette instrument and the Covaris E220 system permits the loading of up to 96 samples for shearing. These instruments are available to users by first contacting the Division and reserving a time.

The Covaris Sonicators are used to give controlled DNA shearing for NGS applications including library preparation and chromatin shearing for ChIP-Seq experiments. 

Covaris SonicatorThe Covaris system uses adaptive Focused Acoustics (AFA) to shear samples. The sample is placed into a cuvette that is in a nuclease-free environment so the introduction of nucleases is minimized. Read More

Fees (Price includes cost of the cuvette)

Covaris S2: $10/sample

Covaris E220: $5/sample + $50/run


Pippen Prep Gel Extraction System​Pippen Prep Gel Extraction System

The Genomics Division maintains the Sage Science Blue Pippen Prep automated gel extraction system. The Pippin Prep is an electrophoresis platform for collection of size-selected DNA samples. The system collects targets between 50 bp – 8 kb, and provides higher quality DNA (with a fraction of the time and labor) than manual gel purification.

The Pippin Prep can significantly improve NGS library preps, and provide more meaningful data per sequencing run. The instrument features a computer-controlled power supply and an integrated optical system, which enables user-defined size fractions to be collected automatically.

Product DNA is eluted into liquid buffer and removed using standard pipettes. The system uses pre-cast disposable agarose gel cassettes, and each cassette can process five samples per run.

Fees

$90 per gel (4 or 5 samples can be run on each gel)


Agilent BioanalyzerAgilent Bioanalyzer

A good quality sample is essential for the successful completion of most sequencing and PCR-based applications. The Agilent Model 2100 Bioanalyzer enables scientists working with nucleic acids to carry out automated quality control, sizing and quantification. The quality assessment analysis provided by the bioanalyzer gives a reliable indication of whether samples are degraded, and if samples submitted for NGS or microarray projects will successfully complete the workflow.

The system uses micro-fabrication technology to transfer samples onto miniature glass chips that contain a network of interconnected channels and reservoirs. Filling the channels with a gel matrix and the wells with buffer or sample allows electrophoresis to be carried out on a miniaturized scale. Sample components are detected by their fluorescence and translated into gel-like images (bands) and electropherograms (peaks).

The system automatically calculates the overall RNA concentration and shows the relative ratios of 18S and 28S ribosomal peaks, along with degradation to determine sample RNA integrity number (RIN). The assigned RIN is independent of sample concentration. The RIN value ranges between 1 and 10. A RIN of 1 represents a completely degraded sample that will likely not work in most experiments (e.g., qPCR, microarray and RNA-Seq). A RIN of 10 indicates there is little if any degradation of the RNA sample would likely work in most experiments. As the RIN drops, the RNA quality worsens, and its ability to work in experiments also drops.

Fees

$6.75 per sample

 

Sample and Liquid Handling Robotics

The Genomics Division operates robotic systems to assist in processing samples for next generation and Sanger sequencing sample preparation as well as basic liquid handling procedures. Instruments are operated by Division personnel, and can be available to support custom liquid handling needs.

Caliper NGS SciCloneCaliper NGS SciClone

he service operates Caliper SciClone Liquid Handling Robots to prepare samples for NGS applications. Currently, these high throughput robots can process up to 96 samples at a time and have been programed to run the methods for the Agilent SureSelect whole exome capture, Agilent SureSelect Custom Capture, Illumina RNA-Seq v2, and Illumina DNA-Seq protocols.

 


Beckman Biomek FXBeckman Biomek FX

The Beckman Biomek FX liquid handling system is used to prepare samples Sanger sequencing as well as custom liquid handling operations. Please contact the Kevin Knudtson if you are interested in perform custom liquid handling operations. 

 


IntegenX Apollo 324WaferGen Apollo 324

The Apollo 324 system is a low-through benchtop instrument that integrates and automates all the library preparation steps. Currently this instrument is configured to support preparation of libraries for DNA-Seq, RNA-Seq and ChIP-seq applications.

Learn more about the IntegenX Apollo 324