Transcriptomics and Molecular Medicine

QCPU Room 1613

Laboratory Scientists: Dr. Charlie Hindmarch

We are set up with the Next Generation Sequencing tools and equipment to take your samples from their starting material to sequenced data. We will customize the project based on your unique needs. Whether you want to start with extraction and quantification, run a rtPCR or just have us sequence completely pooled libraries.

Housed in our genomics laboratory we have the ability to extract nucleic acid, quantify via DropSense, QuBiT or LapChip, build libraries for various sequencing projects and sequence on our Illumina NextSeq 550 where data is uploaded to local, secure CAC servers. Included in our sequencing services is access to expertise to help you sift through your data and make sense of your results

Illumina NextSeq 550 Sequencer

The Illumina NextSeq 550 is the only Sequencer on the market that combines high throughput next generation sequencing (NGS) capability with automated microarray scanning and image file preparation. Different flow cell formats and a suite of reagent configurations enable the NextSeq to sequence between 130 and 400 million reads of (either single-or paired-end reads the latter being specific to Illumina) and adjust read length up to 300bp. The NextSeq is capable of delivering DNASeq, RNASeq, TargetedSeq, ChIPseq data from low sample input in ~30 hours. Importantly, the NextSeq is unique because supports array scanning of up to 12 samples. Currently, the NextSeq 550 System supports Infinium® HumanCytoSNP-12, CytoSNP-850K, and HumanKaryomap-12 BeadChips. - A system that is capable of generating both sequence data and data from Microarray technologies - A system that can accurately produce DNASeq, RNASeq, TargetedSeq, ChIPseq data. - A system that allows users to tailor read length, strandedness, and depth. - A system that produces up to 400 million single-end reads; 800 million paired-end reads - A system that can produce up to 120Gb of sequence - A system that allows for paired-end reads

OpenTrons OT-2

OpenTrons Liquid Handling Robot (OT-2) is a open-source and completely customizable. We can program any type of protocol to meet your applications needs. Our robot is capable of pipetting 2ul to 1000ul and is equiped with a magnet, for purification protocols.

PerkinElmer LabChip

DNA and RNA quantitation and sizing can be done in seconds using automated capillary electrophoresis separation. The LabChip® GX Touch- nucleic acid analyzer’s microfluidic technology generates reproducible, high-resolution data and is optimal for NGS library preparation (smear and fragment analysis) and quality control. RNA and DNA fragment analysis (including cell-free (cfDNA), FFPE, liquid biopsy, and PCR-free samples). Quantitation and qualification for CRISPR fragment analysis. Agarose gel workflows. This equipment is capable of 96, or 384 well configurations.

QuantStudio 3 RT-PCR System

The Applied Biosystems® QuantStudio® 3 Real-Time PCR System is designed for users who need an affordable, easy-to-use real-time PCR system that doesn't compromise performance and quality. The simplified Design and Analysis software is ideal for both first-time and experienced users. When connected to the Thermo Fisher Cloud, the QuantStudio® 3 system provides access to your data wherever and whenever you want. Using proven OptiFlex® technology (featuring 4 coupled channels and white LED) and featuring three independent Veriflex® temperature zones, the QuantStudio® 3 system enables improved data accuracy and sensitivity for a broad range of genomic applications.

NGS Sequencer

We can make libraries for you or run already made libraries. Popular services include:

3' RNA Sequencing
CHIP Seq
16S Sequencing
Bioinformatic Analysis

Liquid Handling Robot

OpenTron Liquid handling robot is an open source code robot, of limitless potential! Our unit comes equiped with 2 robot pipette arms for volumes 20ul and 200ul, it also includes a magnetic plate making it appropriate for applications with magnetic beads. This robot is useful for any protocol involving alot of repeatative pipetting where accurary is paramount, such as standard PCR, qPCR, rtPCR and library purification. The software is user friendly and completely customizable. If you are interested in booking our robot please contact us to set up a consultation

LabChip

Similar to a BioAnalyzer, the PerkinElmer LabChip is a microgel that produces a highly sensitive quantified output that allows you to visualize molecular weights. Our system is equip to run up to 384 well-plates and requires only 2uL of sample input.

rt/qPCR

The QuantStudio 3 is a trendy, and convinent cloud based PCR machine that take 0.2mL, 96 well plates. Users must sign up for a Thermo Cloud account and from there can either create custom runs and labels, or choose from a library of 25 pre-program runs. Users can upload their program directly to QCPU's QuantStudio machine and drop off their sample plates for us to run. If you download the ThermoCloud account to your phone you can keep an eye on your run from anywhere and have you results uploaded directly to your account.

PrawnSeq – QCPU sequenced the Giant freshwater Prawn. Pasookhush, P., Hindmarch, C., Sithigorngul, P. et al. Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) post-larvae in response to M. rosenbergii nodavirus (MrNV) infection: de novo assembly and functional annotation. BMC Genomics 20, 762 (2019). https://doi.org/10.1186/s12864-019-6102-6

In collaboration with the Department of Biology at Queen’s University, Dr Hindmarch worked with Dr Pasookhush in Thailand in order to perform an RNA sequencing project. Dr. Pasookhush’s group wanted to understand the giant fresh water prawn’s (an economically important species) immune response during the post-larval stage when they are susceptible to infection from a debilitating environmental virus. Furthermore, they wanted to provide bio-rationale targets to help contain and restrict disease outbreak. They ran into a major limitation where there is no reference genome for this species. Dr Pasookhush under the supervision of Dr Hindmarch used de novo transcriptome assembly and annotation so that the experimental groups could be compared. This study went from prawn-to-publication in under 1 year.