Our streams
Find out more about the different streams at UCL Genomics, including nucleic acid extractions, quality control, microarrays, sequencing and bioinformatics and more.
The facility can accommodate extraction of high-quality DNA and RNA from a variety of non-infectious sample types through use of a Hamilton Microlab Nimbus with Kingfisher Presto technology for high throughput projects, and smaller scale throughput through our Omega Biotek Magbinder® Fit24 robot. In addition, we can offer methods using the Qiagen EZ2 for sterile site extractions. We currently offer validated, standardised extractions of DNA from whole blood, saliva, cells, fresh-frozen tissue, FFPE tissue, and other human fluid samples. Currently from RNA; whole blood stored in PAXgene tubes, cells and tissue. The team also have experience working with difficult, degraded, or low-input sample types. We welcome both short and long-term projects, with as little as four samples for pilots, to thousands of samples in batches for larger projects.
Contact: ich.genomics@ucl.ac.uk
UCL Genomics has quality control at the core of its operations. The facility houses a comprehensive suite of QC equipment to assess quantification, contamination and purity, integrity and sizing. Nucleic acid quantification is performed on our Invitrogen Qubit/Qubit Flex Fluorometer, where broad range or high sensitivity assays for both DNA and RNA are available. We also house the Agilent TapeStation 4200, offering checks for nucleic acid integrity and sizing. Different assays are available for analysing DNA and RNA of different concentration and sizes: genomic DNA, D1000, or D5000 for DNA; and standard or high sensitivity for RNA.
Contact: ich.genomics@ucl.ac.uk
Our facility offers a range of microarray service provision to both national and international collaborators to deliver high quality data with fast turnaround times. The facility is equipped with dedicated array processing automation through TECAN liquid handling robots and an Illumina iScan with autoloader, enabling large-scale population studies, clinical research, and other human genotyping projects using Infinium and Infinium EX technologies. The team can help with project design, full microarray processing, quality control checks and the provision of initial data outputs.
Contact: ich.genomics@ucl.ac.uk
The facility offers genome-wide DNA methylation profiling using Illumina Infinium Methylation EPIC arrays, Infinium Methylation Screening Array (MSA), and Infinium Mouse Methylation arrays. The facility also can perform bisulfite conversion, FFPE restoration as well as guidance on project design, quality checked data delivery and support with data analysis.
Contact: ich.genomics@ucl.ac.uk
The facility can process custom and commercial PGx panels run on Illumina microarray platforms. Analysis using the Illumina DRAGEN Star allele caller, focuses on drug-response variants to support precision prescribing. Long read sequencing for targeted PGx sequencing available.
Contact: ich.genomics@ucl.ac.uk
The facility houses multiple short-read sequencers to support many applications for projects of varying sizes and can support running flow cells that generate anywhere between 300Mb and 7.5Tb of DNA sequence allowing for applications including whole genome, whole exome, transcriptome & whole genome methylation. UCL Genomics can generate long-read sequence depending on the amount of sequence data required for a particular project. The facility also has several automation platforms, allowing for implementation of high throughput sample preparation for both short and long read sequencing.
Contact ich.zcr.uclg.sequencing@ucl.ac.uk
For comprehensive Long Read Sequencing, contact our partners at the Long Read Sequencing Facility at UCL.
Our pathogen sequencing stream can support:
- Library preparation of whole pathogen genomes and amplicons
- Library preparation for enrichment of pathogen genomes including from clinical or FFPE samples using our own in-house custom design capture probes against a variety of DNA and RNA viruses and bacteria
- SARS-CoV-2 sequencing by targeted enrichment (Agilent), or ARTIC amplicon sequencing (Illumina and Oxford Nanopore)
- 16s rRNA metagenomics
- RNA-Seq for bacterial transcriptome analysis or pathogen discovery
- DNA and RNA metagenomics
Using the 10X Genomics Chromium platform, UCL Genomics offers
- The standard Single Cell Gene Expression solution (3’ Gene Expression)
- Single Cell Immune Profiling (5’ Gene Expression with TCR/BCR sequencing)
- scRNAseq Multiome (GEX and ATAC sequencing)
- GEM-X and GEM-X Flex assays from 10x Genomics.
We support projects utilising Feature Barcode Technology (e.g. CITESeq, CellPlex etc). The facility can accept single cell/nuclei suspensions for processing from suspension QC and Chromium chip loading through sequencing and up to preliminary data analysis (generation of count matrix).
The facility supports spatially resolved gene expression projects using 10X Genomics Visium Assays. These assays provide integration with histological imaging and sequencing for spatial context in gene expression. These assays are suitable for FFPE and fresh frozen tissue.
These solutions include:
- Standard Visium
- Visium HD
- Visium HD PolyA
The facility offers metagenomics profiling from a range of clinical and environmental sample types, including blood, urine, swabs, tissue and others via manual or automated extractions using the Qiagen EZ2 extraction robot.
The facility has dedicated lab space for minimising contamination risk, in addition to dedicated class II microbiological safety cabinet hoods for sterile and non-sterile site samples. Following extractions, samples can be processed for short-read or long-read untargeted metagenomics sequencing, or 16S and 18S rRNA sequencing.
The facility offers Olink Reveal, an NGS-based protein profiling service utilising Proximity Extension Assay (PEA) technology. Olink Reveal provides powerful content at lower cost, targeting 1000+ proteins which covers 100% of top-level pathways, 64% of all pathways, and 96% of immune response pathways. We can offer the entire workflow, from protein library preparation, sequencing, to biological interpretation.
Comprehensive data analysis services across all platforms, including alignment, quantification, differential expression, variant calling, and pathway analysis using tools like IPA and custom pipelines.
Contact ich.zcr.uclg.sequencing@ucl.ac.uk
Software and computing
High-Performance Computing Clusters
Ingenuity Pathway Analysis (IPA) Software
The facility has a dedicated stream for training, workshops and bespoke education sessions on genomic technologies, sample preparation, sequencing methods, and data interpretation - designed for researchers, clinicians, and students.
Contact: Mark Kristiansen (sejjmkr@ucl.ac.uk) in the first instance
Find out more about the UCL MSc programme in Cell, Gene and Novel Therapies at UCL Great Ormond Street Institute of Child Health
Contact: cgt@ucl.ac.uk