INSTRUMENTATION

The Applied Genomics and Bioinformatics is a full service high-throughput genomics facility with instruments for Illumina sequencing-by-synthesis, single cell capture, automated library preparation, automated nucleic acid purification, nucleic acid fragment analysis, focused ultrasonicator, and high-throughout qPCR.  We offer some instruments for self-use.

ILLUMINA SEQUENCERS

Together, our Novaseq 6000, NextSeq 500, and MiSeq suite of Illumina next-generation sequencers provides researchers extreme flexibility in a cost-efficient manner. We offer a wide range of of read capacity, output, and lengths, run times, and costs for different sequencing applications.  Please visit our sequencing-only (links to sequencing-only page under services) page for more information.

NOVASEQ 6000

The NovaSeq 6000 system offers flexibility for virtually any sequencing method, genome, and scale.  Patterned flow cell technology generates an unprecedented level of throughput for a broad range of sequencing applications. Four flow cells are available, as well as the NovaSeq XP workflow that allows for the loading of individual lanes with different library types. Up to 3000 Gb output, 10 B reads, and 2x150 bp read length.

NEXTSEQ 500

The NextSeq 500 system delivers the power and flexibility to carry out applications such as whole genome, exome, transcriptome, and methylation sequencing, among others.  Two flow cell configurations allow for tunable outputs. Up to 120 Gb output, 400 M reads, and 2x150 bp read length.

MiSEQ

The MiSeq system offers the first end-to-end sequencing solution, integrating cluster generation, amplification, sequencing, and data analysis into a single instrument. The MiSeq is best suited for whole genome sequencing of smaller model organism genomes, medium to small targeted panels, amplicon sequencing, 16S metagenomics, quality control of libraries, and more.  Flow cells are available in 3 sizes. Up to 15 Gb output, 25 M reads, and 2x300 bp read length.

MINISEQ

The MiniSeq system delivers the power and confidence of proven Illumina next-generation sequencing technology in an accessible sequencing solution.  It features cost-efficient sequencing, even for low numbers of samples.  Up to 7.5 Gb output, 25M reads, and 2x150 bp read length.

 

SINGLE CELL PLATFORMS

10x GENOMICS CHROMIUM CONTROLLER

The 10x Genomics Chromium Controller performs high-throughput, parallel partitioning, and automated barcoding for powerful RNA, DNA, and epigenomics sequencing applications for up to 80,000 single cells.  Single cell transcriptomics applications include gene expression profiling, simultaneous gene and cell surface protein expression profiling, gene expression CRISPR screening, immune profiling, simultaneous immune & cell surface protein profiling, and immune profiling & antigen specificity.  Combine single cell transciptomics with single cell chromatin accessibility for a multi-omics approach.  Or examine copy number variation of up to 40,000 cells in parallel.  The Chromium Controller also allows for long-range whole genome/exome applications for haplotype phasing & structural variation information, as well as de novo sequencing.

BD BIOSCIENCE RHAPSODY SINGLE CELL SYSTEMS

The BD Rhapsody System profiles gene expression across tens of thousands of single cells in an efficient system that reduces experimentation time and sequencing costs.  Single cell suspensions are loaded onto 200,000-microwell arrays and a bead barcoding system enables single-cell analyses.  Analyze gene expression using BD Rhapsody Human Onco-BC, Mouse Immune Response, Human T-Cell Expression, and Human Immune Response targeted panels.  

 

AUTOMATED LIQUID HANDLERS

FORMULATRIX MANTIS

With a dispense range from 100 nl and a 6 µL dead volume, this non-contact liquid dispenser provides ultimate flexibility for single-cell genomics applications, and assay miniaturization and optimization.  The MANTIS utilizes positive displacement dispensing technology to measure and dispense discrete volumes of liquid with high accuracy and speed.  The user-friendly software allows for quick set up and dispensing into 96-, 384- or 1536-well plates.

EPPENDORF epMOTION 5075 NGS SOLUTION

Combined with a wide choice of ​liquid handling tools, accessories, and application options, the epMotion 5075 NGS Solution system can cover all genomic automation needs, including NGS sample preparation, PCR setup, and sample normalization.​  The highly accurate pipetting system, combined with unique operating features, ensure that the quality of the data generated by pre-optimized and manufacturer-qualified NGS reagent kit methods meets or most often exceeds the stringent kit manufacturer’s qualification guidelines. Change to: The AGCT Core owns two epMotion 5075 NGS Solution systems, for pre-amplification and post-amplification work.

 

NUCLEIC ACID PURIFICATION SYSTEMS

MagNA PURE LC 2.0 INSTRUMENT

The MagNA Pure LC 2.0 Instrument is a tabletop instrument for rapid, cross-contamination-free preparation of nucleic acids and PCR setup. Equipped with a reliable robotic system, it can process up to 32 different samples in a single batch.  The magnetic-bead technology, combined with dedicated kits, enables consistent isolation of high-quality DNA or RNA.  Automatically isolate nucleic acids from whole blood, white blood cells, bacteria, tissue, and other difficult samples.

 

SONICATORS

COVARIS M220 FOCUSED-ULTRASONICATOR

The Covaris focused-ultrasonicator uses the Adaptive Focused Acoustics® (AFA) process to deliver high frequency, accurately focused, and specifically targeted acoustic energy to samples for a variety of application areas including: DNA shearing for next-generation sequencing, RNA and protein extraction, chromatin shearing, and cell lysis.  The characteristics of the instrument enable a highly reproducible and isothermal process, reducing experimental variation and heat-induced damage to the sample.

 

FRAGMENT ANALYZERS

AGILENT 2100 BIOANALYZER

The 2100 Bioanalyzer system is an established automated electrophoresis tool for the sample quality control of DNA and RNA. Together with the 2100 Expert Software and Bioanalyzer assays, the 2100 Bioanalyzer provides highly precise analytical evaluation of various samples types in many workflows, including next generation sequencing (NGS), gene expression, biopharmaceutical, and gene sediting research. 

AGILENT FRAGMENT ANALYZER

The Fragment Analyzer is an automated parallel capillary electrophoresis that provides reliable quality control (QC) for nucleic acids. ProSize data analysis software provides quick and easy visual analysis of DNA and RNA quality, reporting size, concentration, and quality metrics of DNA and RNA fragments.  ProSize software can be used to analyze a wide range of nucleic acids, including genomic DNA, NGS libraries, plasmids, microsatellites, PCR amplicons, restriction enzyme digests, mRNA, and total RNA.  The Fragment Analyzer allows for the high-throughput analysis of up to 288 samples.

AGILENT 4200 TAPESTATION

The Agilent 4200 TapeStation system is an automated electrophoresis tool for DNA and RNA sample quality control. Fully automated sample processing enables the unattended analysis of size, concentration and integrity. Analyze any sample number between 1 and 96.  The TapeStation system provides a complete solution for true end-to-end sample quality control within any next-generation sequencing workflow.

 
 

REAL-TIME PCR SYSTEMS

APPLIED BIOSYSTEMS QUANTSTUDIO 12K FLEX

The QuantStudio 12K Flex Real-Time PCR System is a highly flexible, comprehensive real-time PCR platform that leverages the best of Applied Biosystems real-time technology in a single instrument. The system includes easy-to-change blocks that can accommodate OpenArray plates, TaqMan array cards, 384-well, and 96-well plates.

FLUIDIGM BIOMARK HD

Fluidigm’s BioMark HD technology utilizes thousands of intertwining microfluidic valves and channels on a silicon chip to automatically combine samples, reagents, and primer-probe sets into thousands of PCR reactions using significantly smaller reagent volumes as compared to traditional real-time PCR systems.  Interrogate up to 48 genes in 48 samples (48x48) or 96 genes in 96 samples (96x96).

 

NUCLEIC ACID QUANTIFICATION SYSTEMS

INVITROGEN QUbIT 2.0 AND 3.0 FLUOROMETER

Benchtop fluorometer designed to accurately measure DNA, RNA, and protein quantity with more sensitivity and accuracy than UV absorbance.

THERMO SCIENTIFIC NANODROP 8000

High throughput efficiency and accuracy.  The Nano Drop 8000 delivers full-spectrum, micro-volume UV-Vis absorbency measurements for up to eight samples at one time.