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GENOMICS

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Globally, the demand for genomics workflows is growing exponentially. The Hugh Green Technology Centre is responding to this demand by expanding its genomics capabilities to deliver innovative and reliable genomic services to support both the research and clinical trials markets across New Zealand.

​The Hugh Green Technology Centre is equipped with the 10x Genomics Chromium iX and BD Rhapsody Express instruments for preparing single-cell cDNA libraries. These platforms enable us to conduct single-cell RNA sequencing workflows, allowing simultaneous sequencing of up to 20,000 cells. Additionally, we use the MinION and PromethION P2 Solo systems from Oxford Nanopore Technologies for long-read sequencing.

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SINGLE CELL RNA SEQUENCING

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10x Genomics Chromium iX

We have enhanced our single-cell RNA sequencing capabilities with the acquisition of the 10x Genomics Chromium iX instrument. The 10x genomics workflow for scRNAseq enables 3’ and 5’ WTA sequencing, BCR/TCR sequencing, scATACseq, and CRISPR screening.  This system can capture both cells and nuclei, it is compatible with fresh and frozen samples and with FFPE-fixed cells if using the probe-based Flex system, which can capture about 19,000 genes and be customised with additional probes. Some assays also allow for simultaneous antibody-oligo capture to interrogate the proteome.

BD Rhapsody

The BD Rhapsody Express is used for capturing single cells for single-cell RNA sequencing via a gentle microwell capture procedure. Libraries are prepared and quality controlled in-house before being sent to an external sequencing provider of your choice. Our Data Science team can support data analysis, or clients can perform it independently.

 

BD Rhapsody Express can be paired with optional data QC by Seven Bridges. BD recommends SeqGeq, a desktop bioinformatics platform with an intuitive interface, for complex scRNA-seq analysis. 

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SPATIAL TRANSCRIPTOMICS
 
Visium HD with CytAssit

Spatial discovery with Visium HD Spatial Gene Expression.

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See your tissue in high definition: 

  • Whole transcriptome analysis at single cell-scale resolution

  • Continuous tissue coverage

  • Best-in-class data powered by innovative probe-based chemistry and a Visium CytAssist-enabled workflow.

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The Visium HD features 2µm barcoded capture squares, while the standard Visium offers a 100µm spot-to-spot distance. Both allow for whole transcriptome analysis (WTA) overlaid on H&E or immunofluorescent staining. Capture areas of 6.5 x 6.5 mm and 11 x 11 mm are available.

 

The Visium HD, detects approximately 18,000 unique genes and is available for mouse and human samples. The classic Visium offers polyA tail capture and probe-based assays, with some assays compatible with antibody-oligo capture. Depending on the assay, fresh frozen, fixed frozen, or FFPE samples can be used. The CytAssist Instrument optimises tissue transfer from standard glass slides to the Visium capture slides and allows for better resolution.

DIGITAL DROPLET PCR

 

The Hugh Green Technology Centre offers advanced digital droplet PCR (ddPCR) capabilities utilising the BIORAD QX200 Droplet Digital PCR System. This method leverages water-oil emulsion droplet technology, wherein a sample is partitioned into 20,000 droplets, with PCR amplification occurring in each individual droplet. The ddPCR technology employs reagents and workflows analogous to those used in standard TaqMan probe-based assays, with massive sample partitioning being a critical feature of the ddPCR technique.

 

ddPCR is particularly advantageous in scenarios where PCR inhibitors may be present, such as in faecal samples. It has been effectively used in wastewater testing for COVID-19 detection, where both template quality and quantity are low, and PCR inhibitors are prevalent. A significant benefit of ddPCR over qPCR is the elimination of the need for a standard curve, as ddPCR directly counts template molecules, providing an absolute measure of concentration.

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The ddPCR System can be used to:

  • Detect rare DNA target copies

  • Determine copy number variation

  • Measure gene expression levels

  • Digital droplet PCR machine

 

Applications of the QX200 Droplet Digital PCR System include:

  • Cancer biomarker studies and copy number variation 

  • Pathogen detection

  • Next generation sequencing

  • Gene expression analysis

  • Environmental monitoring

  • Food testing

OXFORD NANOPORE LONG-READ SEQUENCING 

 

We use the MinION and PromethION P2 Solo from Oxford Nanopore Technologies for long-read sequencing.

Nanopore sequencing involves passing a long polymer through a protein pore using an electric current to detect changes in translocation speed, which vary based on the DNA base. This rapid, continuous method allows for efficient DNA sequencing.

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The MinION and PromethION P2 Solo sequencers use consumable flow cells with 2,048 sequencing wells (MinION). Each well has a polymer membrane with embedded protein pores. An electrical potential across the membrane drives ion flow through the nanopore, sequencing DNA.​

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​At any time, 512 wells (MinION) are connected to sensing circuits, capturing 4,000 snapshots per second (4 kHz) and measuring up to 450 DNA bases per second, yielding up to 40 gigabases from a two-day run.

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  • MinION Flow Cell: up to 50 million Gb of data

  • PromethION Flow Cell: up to 290 million Gb of dat

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CONTACT US

Malaghan Institute of Medical Research
Gate 7, Victoria University
Kelburn Parade, Wellington

 

PO Box 7060
Newtown, Wellington 6242
New Zealand

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