Iowa Institute of Human Genetics

  • Quality Control and Support Instrumentation

    Sample Preparation

    NanoDrop 1000

    NanoDrop 100The 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

    Corvaris S2The 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.

    Corvaris E220The 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 ExtractionThe 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 Bioanalyzer

    Agilent BioanalyzerA 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 SciClone

    Caliper SciCloneThe 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 FX

    Beckman BiomekThe 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 324

    Integen Apollo 324The 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

     

     

    NuGen Mondrian SP+

    NuGen Mondrian SPThe NuGen Mondrian SP+ system is used by the Division to prepare samples for ChiP-Seq and RNA-Seq applications in which the amount of sample provided is very small, as little as 0.1 ng. The Mondrian SP+ System from NuGEN is an innovative new approach to sample preparation based on the use of digital microfluidics for liquid handling. Sample preparation is performed in sub-microliter volumes within low cost, disposable cartridges. The system provides plug and play automation with a simple user interface and load-and-go cartridge operation to significantly reduce the hands-on time for genomic sample preparation. Read More