Services
Our single cell analyses would have been impossible without the great help and support of the NU Genomics Core Facility. They are involved from the initial stages of experimental design to delivering high quality data at record times, and being closely involved in proposal and manuscript preparation.
Majlinda Lako, Professor of Stem Cell Science, Newcastle University
The Genomics Core Facility have expert knowledge in study design and application delivery using the following platforms:
Next-Generation Sequencing
The GCF Illumina MiSeq, NextSeq 500 and NovaSeq 6000 platforms offer the ultimate in sequencing scalability to suit a range of project sizes and budgets.
We provide dedicated library preparation and sequencing pipelines, such as:
- Genome analysis, including amplicon, exome, and genome sequencing
- Transcriptome analysis including mRNA and Total RNA sequencing
- Epigenome analysis including ChIP-Seq (chromatin immunoprecipitation)
- EM-Seq (methylation profiling)
Team members are available for consultation on novel 'proof-of-principle' projects.
The lab also provides a 'sequencing only' service for customer prepared libraries.
Single-Cell Applications and Spatial Transcriptomics
Single-Cell
Working closely alongside our colleagues in the Flow Cytometry Core Facility and Bioinformatics Support Unit, the GCF maintains a state-of-the-art single-cell isolation and sample processing lab, equipped with the 10X Genomics Chromium platform and Fluidigm C1.
Our services include:
- expression analysis
- immune profiling
- ATAC (Assay for Transposase-Accessible Chromatin) applications
- 'Plate-based' single-cell and enriched 'mini-bulk' (10-1000 cells) mRNA-Seq and Total RNA-Seq
All GCF single cell applications are delivered as an end-to-end service.
For users wishing to isolate rare cells from complex tissue samples, the facility offers access (training included) to the Leica LMD7 (laser-capture micro-dissection).
In addition, the Chromium controller can be made available (training included) to Newcastle University staff working on 'fresh from theatre' samples (including pre-arranged out-of-hours access).
Spatially Resolved Transciptomics At Newcastle (SpaRTAN)
Spatial Transcriptomics is a powerful technology combining the disciplines of histology, imaging and NGS data analysis, enabling researchers to overlay and visualise gene expression (mRNA) in context with a tissue section.
One of only a few Certified Service Providers offering the Visium technology from 10X Genomics, Newcastle University is able to provide an end-to-end service by combining the expertise of several specialist units.
Real-Time PCR and Droplet-Digital PCR
The GCF offers scalable droplet-digital PCR using the BioRad QX200 AutoDG (up to 96 reactions per run), and real-time PCR using the BioRad CFX Touch (up to 96 reactions per run) and the Fluidigm BioMark HD (up to 9216 reactions per run).
Commonly used for target validation and high-throughput screening, all three instruments are available (training included) as 'open access' platforms.
Options for analysis include:
- Copy number variation
- Rare variant detection
- Gene expression
- miRNA abundance
- CRISPR screening
Sample QC and Training
The team utilise a range of instruments to assist with DNA or RNA sample processing. The Agilent TapeStation 4200 and PerkinElmer LabChip GX Touch HT are used for sample or sequencing library quality assessment. The Diagenode Bioruptor Pico is used where samples require fragmentation.
All three instruments are available (training included) as 'open access' platforms.
The facility is organised around task-specific work areas, comprising five dedicated labs. This offers flxibility to accommodate colleagues during training sessions or instrument / application demonstrations.