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Quality Control and Support Instrumentation

Sample Preparation

NanoDrop 1000​NanoDrop 2000

The NanoDrop 2000 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.

 


​Qubit 


Invitrogen Qubit assays use target-selective dyes that emit fluorescence only when bound to their DNA, RNA, or protein target. They are more accurate than traditional UV absorbance, which can overestimate sample concentrations due to contaminants such as salts, solvents, detergents, proteins, and free nucleotides. 

The Qubit Fluorometer is available on a first come, first-served basis, free of charge. Users are asked to purchase their own kits and prepare their samples and standards before coming to the core to measure.  Please note you will need a way to record your results. 

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


Covaris Sonicators

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.

Covaris Sonicator

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

The 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 

Covaris S2 Instrument Fee: $5/run

Covaris E220 Instrument Fee: $60/run

Covaris Tubes: $7/tube 


Sage Science BluePippin

The Genomics Division maintains the Sage Science BluePippin DNA Size Selection for Next-Gen Sequencing, with Pulsed-Field (100bp – 50kb).

The BluePippin has the DNA capabilities of the Pippin Prep, plus the extra benefit of pulsed-field electrophoresis for resolving and collecting high molecular weight DNA.  For long-range genomic applications, high-pass filtering allows users to collect all fragments above a size threshold set by the user.

Target sizes or ranges of sizes are entered in software, and fractions are collected in buffer. Up to 5 samples/gel cassette may be run, with no possibility of cross contamination. https://sagescience.com/products/bluepippin/

Fees

Full Service: $100.00 + $70.00/gel (up to 5 samples/gel)

Self-Service:  Instrument Fee $10.00 + $70.00/gel (as needed)


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

RNA Pico Bioanalyzer:  $12.00/sample

RNA Nano Bioanalyzer:  $12.00/sample

DNA High Sensitivity Bioanalyzer:  $12.00/sample

DNA 1000 Bioanalyzer $77.00/chip


Agilent TapeStation 

The Agilent 4150 TapeStation system is a low-throughput automated electrophoresis platform for nucleic acid sample quality control. It allows a quick, easy, and reliable analysis of DNA and RNA samples for up to 15 samples per run.  

The TapeStation system uses ready-to-use ScreenTape technology to perform nucleic acid analysis with excellent reproducibility for size, concentration, and integrity. Each sample is analyzed in an individual lane, eliminating potential contamination and carryover. Analysis uses as little as 1 to 2 µL of DNA and RNA samples, even for high-sensitivity assays. There is a wide range of RNA and DNA ScreenTape applications. 

ScreenTape technology offers a broad assay portfolio and known quality metrics to analyze sample quality and NGS libraries, such as RNA and DNA Integrity Numbers (RIN & DIN). Results can be displayed as an electropherogram, as a gel image, or in tabular format for effortless sample comparison. 

Fees  

RNA/DNA High Sensitivity TapeStation:  $12.00/sample 

gDNA TapeStation: $12.00/sample 


Agilent Fragment Analyzer 

The Agilent 5300 Fragment Analyzer system is a capillary electrophoresis instrument that can analyze up to 47 samples + ladder in parallel. DNA or RNA fragments are fluorescently labeled, separated by capillary electrophoresis (CE), and sized by comparison to an internal standard. Applications include initial assessment of RNA/DNA sample integrity, as well as sizing and quantification of final NGS libraries.  

During the electrophoresis process, individual capillaries are filled with gel that serves as the separation matrix. Samples are voltage-injected into the capillaries and each sample moves through an individual capillary in a size-dependent manner. As the fragments pass the detection window, a detector captures the size and concentration level of the sample. This series of images is then merged together to produce a high-resolution electropherogram across the entire sizing range. 

Depending on input sample type, quality assessments including RNA Quality Number (RQN), Genomic Quality Number (GQN), sample size, and concentration may be provided. 

Fees 

Cost per run of up to 48: $325.00 



Sample and Liquid Handling Robotics 

The Genomics Division operates robotic systems to assist in processing samples for NGS library prep, Sanger sequencing sample preparation, and basic liquid handling procedures. Instruments are operated by Genomics Division personnel. 

Caliper NGS SciClone

 

 Caliper NGS SciClone 

The Caliper NGS SciClone has the following methods available: Agilent SureSelect Whole Exome Capture, Agilent SureSelect Custom Capture and Sanger bead clean-up protocols. 

 

 


 Eppendorf epMotion 5075  

The Eppendorf epMotion liquid handler uses customized automation methods for Illumina RNA-seq and KAPA DNA-seq library prep. 

 Library prep fees can be found here