Equipment

10X Genomics Chromium Controller

The Chromium Controller instrument performs the integral first step in constructing 10x Genomics single cell NGS libraries by creating the emulsion bubbles in which single cells are isolated and individually tagged with a unique 16nt barcode. Current applications include 3′ Single cell RNA-seq, 5′ single cell RNA-seq with or without additional VDJ immune profiling (B cell or T cell) and cell surface feature barcoding libraries (allowing more than one individual sample to be multiplexed into a single library, thus saving on reagent and prep costs), ATAC-seq, and cell surface protein to RNA transcript association analysis (same workflow as the previously mentioned feature barcode multiplexing strategy). Up to 10,000 cells can be captured per library, allowing for deep profiling of complex cell populations. This instrument is core operated only.

10X Genomics Chromium for single cell isolation

Illumina NextSeq 2000 Sequencing System

The NextSeq 2000 is Illumina’s latest advancement in Next Generation Sequencing (NGS) benchtop instrumentation.  It operates the P2 patterned flow cell which has an output of 400 Million reads per run, similar to the High Output flow cell of the NextSeq 500 for a similar run time.  The same instrument is engineered to run the P3 flow cell with an output of 1 Billion reads (300 Gb) per run or 2.5X the capacity of our previous NextSeq 500  instrument. The P3  yields a number of clusters that is between the High-End NovaSeq 6000’s SP and S1 flow cells.

More information can be found on the Planning an NGS Experiment page.

Applications

  • Whole-genome resequencing
  • Targeted resequencing, including exome panels and custom enrichment panels (100s kb–Mbs)
  • Whole-genome de novo sequencing
  • Sequencing of bisulfite-treated DNA (Methyl-Seq)
  • RNA sequencing (RNA-Seq), including mRNA sequencing and total RNA sequencing (coding and noncoding)
  • Genotyping by sequencing
  • Nucleosome positioning and chromatin structure studies
  • ChIP-Seq: studying sequence-specific protein–RNA interactions
  • Sequencing of ancient DNA samples
  • Single-cell applications including RNA-Seq, VDJ, Cell surface expression, ATAC-seq
  • Linked long-read applications

10X Genomics Chromium for single cell isolation

Illumina MiSeq Sequencing System

The miSeq desktop sequencer allows access to more focused applications such as microbiome sequencing (bacterial and fungal), amplicon sequencing, metagenomics, and small genome sequencing, starting with 10ng of DNA. New MiSeq reagents enable up to 25 million sequencing reads and 2×300 bp read lengths.

MiSeq Sequencing System

Nanopore GridION


The Oxford Nanopore GridION is a flexible benchtop sequencing and analysis device designed to run and analyse up to five individually addressable MinION or Flongle Flow Cells. It is ideal for labs with multiple projects that need the advantages of nanopore sequencing: simple library preparation, real-time analysis and new biological insights from long reads. The GridION also allows users to offer nanopore sequencing as a service.

Qiagen QIAcuity Digital PCR System

The QIAcuity is a nanoplate-based system which seamlessly integrates a standard dPCR workflow of partitioning, thermocycling and imaging into a walk-away automated platform with minimal hands-on time.The QIAcuity system makes absolute quantification accessible, affordable and easy for all laboratories. The walk-away automation integrates and streamlines the entire digital PCR workflow into single instrument with minimal hands-on time. It is also easy to adapt your current qPCR assays to the QIAcuity Digital PCR System. No change in plate handling is required when coming from qPCR, assuring fast assay setup and quick results in under 2 hours.

The QIAcuity Digital PCR System will deliver precise and multiplexed quantification results for all molecular applications including but not limited to the following research areas:

  • -Rare mutation detection
  • -Copy number variation analysis
  • -Gene expression analysis
  • -NGS library quantification
  • -Pathogen detection
  • -Genotyping
  • -miRNA research

-and many more!

Applied Biosystems QuantStudio 6 Flex Real Time PCR System

The QuantStudio 6 performs both SYBR Green and TaqMan qPCR. Real-time quantitative PCR (qPCR) is a highly sensitive and specific method for SNP genotyping and for amplifying, detecting and quantitating target transcripts.  The QuantStudio 6-Flex enables detection as small as 1.5-fold changes in singleplex reactions and with 10 logs dynamic range.  It can also be used to identify new variants quickly and accurately with high resolution melt.

QuantStudio 6 Flex Real Time PCR System

Agilent Bioanalyzer and Tape Station

The Agilent 4200 TapeStation system is an automated electrophoresis tool for assessing size, quality, and concentration of up to 96 DNA or RNA samples per run. This instrument is commonly used to QC RNA prior to RNAseq library prep and to QC finished NGS libraries. The core currently stocks a variety of kits for analyzing RNA and DNA of both high and low concentrations. This instrument is both Core and user operated, but requires user training before use.

The Agilent Bioanalyzer uses a microfluidic chip to perform similar analyses to the TapeStation. This instrument is currently only available for special request runs of a type that are not supported by the Agilent TapeStation. Please inquire.

Agilent 4200 TapeStation system
Agilent BioAnalyzer

NanoVue spectrophotometer

The GE HealthCare NanoVue performs spectrophotometric absorbance readings of small volumes for the quantitation of RNA and DNA. This instrument is Core operated.

NanoVue spectrophotometer

Qubit 3.0 fluorometer

The Qubit 3.0 Fluorometer performs fluorescence based quantitation of DNA and RNA samples. The Core currently stocks the dsDNA HS kit, but other kits are available upon request or can be user supplied.

Qubit fluorimeter

Covaris S2

The Covaris S2 shears nucleic acids into suitably sized fragments for NGS library prep using focused acoustic energy. Protocols are available for shearing DNA to sizes of 150 to 1500 base pairs. This instrument is user operated only.

Covaris S2