Next Generation DNA Sequencing (NGS) Instruments
The UNMC NGS Core facility is a comprehensively equipped facility that serves the regional research community. The core operates the Illumina NextSeq500, NextSeq550, and MiSeq systems. (Illumina, San Diego, CA).
NextSeq500 and NextSeq550- The NextSeq Series delivers the power of high-throughput sequencing with the speed, simplicity, and affordability of a benchtop next-generation sequencing (NGS) system
https://www.illumina.com/systems/sequencing-platforms/nextseq.html
MiSeqV2 - The MiSeq System facilitates your research with a wide range of sequencing applications. It is capable of automated paired-end reads and up to 15 Gb per run, delivering over 600 bases of sequence data per read. The library prep kits that it uses are optimized for a variety of applications, including targeted gene, small genome, and amplicon sequencing, 16S metagenomics, and more.
https://www.illumina.com/systems/sequencing-platforms/miseq.html
Sanger Sequencing
Applied Biosystems (ABI) 3730 DNA Analysis Instrument (Life Technologies, Grand Island, NY). The ABI 3730 instrument is used for sequencing DNA in a variety of contexts such as plasmids and PCR fragments. The Core provides Sanger sequencing services for 90 to 100 different laboratories annually.
Single Cell Genomics Instrumentation
The Genomics Core Facility at UNMC has the instrumentation necessary to enable single cell genomics experimentation. The instruments include the C1 from Fluidigm and the 10x Genomics System. Collectively these instruments facilitate the performing of mRNA or DNA Seq measurements from single cells.
10x Genomics: The 10x genomics system can be used for either single cell RNA expression experiments or generation of DNA libraries for long range DNA information including for sequencing genomes. Thousands of individual cells can be captured simultaneously and individually barcoded for RNA seq. In addition this system can capture individual long molecules of DNA for DNA sequencing. https://www.10xgenomics.com/
C1 Single-Cell AutoPrep System: The C1 is a proprietary microfluidic based system that was designed to isolate and prepare individual cells for single cell genomic analysis. The C1 can capture and enrich up to 96 single cells simultaneously in preparation for downstream analysis. The C1 instrument then lyses the cells, and performs the isolation of the nucleic acids (either RNA or DNA). This system will generate full length cDNA from individual cells. https://www.fluidigm.com/products/c1-system
Nanostring
The nCounter® platform provides a simple and cost effective solution for multiplex analysis of up to 800 RNA, DNA, or protein targets from your precious samples.
Robotics / Liquid Handling for NGS Library Construction
SciClone NGS Library Production Robot (Perkin Elmer): This instrument is used for producing NGS libraries for sequencing. The Sciclone® G3 NGS / NGSx workstations are the most capable automated solution for high-throughput sequencing sample preparation. Built on the Sciclone G3 platform, the NGS / NGSx Workstation is a complete benchtop solution for library prep, sequence capture, and normalization.
http://www.perkinelmer.com/product/sciclone-g3-ngs-workstation-cls145321
Eppendorf 5075 Liquid Handing Robot (Eppendorf North America, Inc., Hauppauge, NY): The EpMotion 5075 automated pipetting system from Eppendorf is used for generating NGS libraries.
qPCR Instruments
Applied Biosystems VIIa Real Time PCR Instrument (Life Technologies, Grand Island, NY). The instrument is utilized for real time PCR, quantification of gene expression and validation of gene expression identified by microarrays or NGS. It is also valuable for the quantification of NGS libraries prior to sequencing.
https://www.thermofisher.com/us/en/home/life-science/pcr/real-time-pcr/real-time-pcr-instruments/viia-7-real-time-pcr-system.html
BioMark HD system: The BioMark is a microfluidic-based, high throughput qPCR system that offers capabilities for gene expression, SNP genotyping, single cell gene and miRNA expression, Copy Number Variation, and digital PCR.
https://www.fluidigm.com/products/biomark-hd-system
DNA / RNA Quantification and Sizing Instruments
Fragment Analyzer Automated CE System: (Advanced Analytical Technologies, Inc. Ames, IA): The Fragment Analyzer™ Automated CE System has been shown to have both better sizing and quantification accuracy/reproducibility than any other analytical methods. This instrument works well for sizing nucleic acids extracted from tissues as well as from single cells in a high throughput fashion. https://www.aati-us.com/instruments/fragment-analyzer/
Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA): The Bioanalyzer instrument is used in a variety of NGS applications, including initial RNA integrity assessments as well as checking the size distribution of libraries for NGS applications. http://www.genomics.agilent.com/en/Bioanalyzer-System/2100-Bioanalyzer-Instruments/?cid=AG-PT-106
Nanodrop Spectrophotomer Instrument: This instrument is used for measuring the concentration and purity of nucleic acids prior to using them in experiments. https://www.thermofisher.com/order/catalog/product/ND-2000
Qubit Instrument: The Qubit is used for measuring double stranded DNA for use in NGS experiments. https://www.thermofisher.com/us/en/home/industrial/spectroscopy-elemental-isotope-analysis/molecular-spectroscopy/fluorometers/qubit.html
DNA Shearing Instrumentation
Covaris S220 Ultrasonicator (Covaris Inc., Woburn, MA): The Covaris S220 Ultrasonicator is used to generate DNA fragments prior to library generation. Next-Gen Sequencing has quickly become one of the most important tools in genomics research and nucleic acid fragmentation is a crucial first step in the sequencing workflow. http://covarisinc.com/applications/dnarna-shearing-for-ngs/
Bioinformatic Resources at UNMC Campus
The Genomics Core interfaces extensively with the Bioinformatics and Systems Biology Core at UNMC. This is an important resource for assistance with analysis as additional PhD and MS level analysts are available for consultation.