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 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 Connect

The Chromium Connect automates 10x Genomics’ scRNA-Seq assay, going from single cells to sequencing-ready libraries with minimal sample handling using an integrated and validated solution. Reduce errors from manual pipetting and minimize technical variation to generate consistent and reproducible single cell gene expression results across experiments, users, and sites. Run up to 8 samples in parallel and capture from 500-10,000 cells per sample.

Mission Bio Tapestri

Explore mutational diversity on a cell-by-cell basis using the Tapestri single cell targeted DNA-Seq platform. Detect SNVs and CNVs in the same cell, or DNA and protein for a multiomics approach. The Tapestri platform can be used to detect rare subclones (down to 0.1%), identify true mutation co-occurance in clonal populations, resolve zygosity, and reconstruct phylogenetic lineages. Compatible with fresh or frozen cells or tissue, as well as methanol fixed cells. Capture from 5,000-10,000 cells. Pre-designed and custom panels available.

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.

 

Sample Preparation and Nucleic Acid Purification Systems

Miltenyi Biotec gentleMACS™Octo Dissociators with Heaters

Fully automate and standardize your tissue dissociation or homogenization of up to eight samples simultaneously. Tissue dissociation is performed in a closed and sterile system. Ready to use programs, in conjunction with Miltenyi tissue dissociation kits that combine mechanical dissociation and enzymatic treatment, yield single-cell suspensions with excellent viability and preserved epitope integrity.  Use the gentleMACS™Octo Dissociators with Heaters upstream of your single cell genomics analyses.

 

S2 Genomics Singulator100

Automated, reproducible, hands-off tissue dissociation from fresh, frozen, or OCT-embedded tissue into single cells or singlenuclei.Choose from a selection of automated pre-set protocols and pre-formulated reagents, or create your own protocols and use your reagents of choice.  The Singulator allows researchers to reproducibly prepare suspensions of high viability cells or nuclei in high yield and from small samples.  Use the Singulator 100 upstream of your single cell genomics analyses.  

 

Miltenyi Biotec autoMACS® Pro Separator

The autoMACS®Pro Separator, in combination with Miltenyi MACS®MicroBeads, provide fast, reproducible, automated cell isolation of virtually any cell type.  The Pro Separator is compatible with automated or manual cell labeling, with the ability to process up to 6 samples in a single run.  MACS®MicroBeads offer cell separation with maximal purity and recovery, with no cell stress and high cell viability using column-based magnetic cell isolation.  Use the autoMACS®Pro Separator and MACS®MicroBeads upstream of your single cell genomics analyses.

 

Miltenyi MACSQuant® Tyto Sorter

The MACSQuant®Tyto Sorter offers a revolutionary way to sort your cells.  Unlike during conventional droplet sorting procedures, cells do not experience high pressure, are not decompressed, and no charge is applied, resulting in great viability and functionality of cells.Samples are kept contamination-free within the disposable, fully closed MACSQuant®Tyto Cartridge, with no risk of carry-over or contamination of fluidics. The sorter is equipped with 3 lasers, allowing for 10-parameter cell sorting.Use the MACSQuant®Tyto Sorter upstream of your single cell genomics analyses.  

 

Miltenyi MACSQuant® Analyzer 16 Flow Cytometer

The MACSQuant®Analyzer 16 Flow Cytometer offers revolutionary automation of flow cytometers.  Fully automate cell staining, data acquisition, and data analysis.  Automated sampling can be achieved from single tubes, multiple tubes, or a 96-well plate.  Select from 14 fluorescence channels.  Use the MACSQuant®Analyzer 16 Flow Cytometer upstream of your single cell genomics analyses.  

 

Qiagen QIACube

Using the same spin columns and steps as the manual procedure, the QIACube automates all steps of the nucleic acid and protein purification procedure.  With no change in purification chemistry, standardized results are ensured whether performing the purification manually or automatically.

 

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. The AGCT Core owns two epMotion 5075 NGS Solution systems, for pre-amplification and post-amplification work.

 

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 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.

 

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.

 
 

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.

 

Real-Time PCR Systems

Applied Biosyetems 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).