Sequencing Platforms
The UCD Conway Genomics Core is currently offering the following:
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The Genomics Core provides access to state of the art, multi-platform Next Generation Sequencing (NGS) based technologies. Next Generation Sequencing has driven major advances in Genomics led research over the past 2 decades and now routinely underpins many research studies across a variety of disciplines. The Genomics Core offers access to both short read (Illumina) and long read (Oxford Nanopore) NGS platforms, including a 10 X Genomics single cell sequencing system.
Illumina NextSeq 500 Platform
The Illumina Platform delivers powerful high-throughput next generation sequencing of short reads with speed and efficiency. Utilising Illumina’s proprietary sequencing-by-synthesis technology and reversible terminator chemistry, it enables the parallel sequencing of millions of DNA fragments with exceptional accuracy.
The NextSeq is easily configured, providing researchers with scalability to handle various project sizes. Based on read length and coverage needs, researchers can choose between multiple flow cell configurations, easily shifting from low- to high-throughput with each sequencing run. Currently, the system can generate up to 120 GB/800 million reads in one 2 x 150bp paired end run.
The platform is fully integrated with Illumina’s BaseSpace Sequence Hub cloud, which allows streamlined run management, primary data analysis/QC and data transfer from a single source.
Applications
A broad menu of sequencing applications is supported including, RNA-seq, exome, small whole genome, targeted resequencing and single cell analysis. https://emea.illumina.com/systems/sequencing-platforms/nextseq.html
Expertise & Services
The Genomics Core provides a range of NGS technical services to researchers including advice on initial experimental design and costs for grant proposals. For further information please contact us to discuss your work or fill out the following enquiry form.
We offer 2 main services:
Full Library Preparation: We offer a Full Library Preparation to Sequencing Service and have experience in a wide variety of Library Generation Protocols including the following:
- mRNA/Whole Transcriptome
- Whole Genome
- Amplicon
- Exome
- ChIP Seq
Sequencing Only Service/Training
The Genomics Core can facilitate the sequencing of user prepared libraries. We also offer a comprehensive training program for researchers who wish to become independent users of the NextSeq platform, allowing flexibility of access to the system. Ongoing technical support is available to all fully trained users.
Please note: In both cases FASTQ demultiplexed data is transferred to the user via the Illumina Cloud, with options available for Secondary data analysis.
Contact
Ms Alison Murphy
T: (+353-1) 716 6955
E: alison.murphy@ucd.ie
Oxford Nanopore Technologies MinION
The Genomics Core offers Nanopore Sequencing utilising Oxford Nanopore Technologies MinION. The platform enables high throughput long read sequencing of DNA and RNA samples in real-time.
The technology utilises Protein Nanopores which allow the sequence of DNA/RNA strands to be read by measuring the individual change in current exhibited by each base in a strand as it passes through a pore. https://nanoporetech.com/how-it-works
One of the main advantages of the technology is the Ultra Long Read lengths produced which greatly improves de novo genome assemblies, structural genomic variant and transcriptomic studies. Also, as sequencing is in real-time it can be stopped as soon as sufficient data is gathered.
Applications
Nanopore Sequencing has been successfully used in the areas of disease surveillance, enviromental monitoring and the identification of food chain pathogens. Protocols are available for the following sequencing applications, whole genome, targeted resequencing, RNA-sequencing (direct/cDNA), Metagenomics, Epigenetics.
Expertise & Services
The Genomics Core Facility provides a range of technical services to researchers including advice on initial experimental design, library preparation protocols, QC and results analysis. Researchers interested in using the MinION are encouraged to contact the Genomics Core to discuss prospective projects.
A full service is provided, from library generation to sequencing, across the application range.
Contact
Ms Alison Murphy
T: (+353-1) 716 6955
E: alison.murphy@ucd.ie
Single Cell Sequencing- 10x Genomics Chromium Controller
Single cell sequencing allows genome and transcriptome analysis of individual cells, providing a high-resolution view of cell-to-cell variation. This highly sensitive technology enables researchers to explore the distinct biology of individual cells in complex tissues and understand cellular subpopulation responses to environmental cues.
The 10x Chromium Controller is a benchtop single cell library preparation system. The platform utilises advanced microfluids to generate tens of thousdands of single cell partitions, each containing an identifying barcode for downstream analysis. Partitioning events occur on a microfluidic chip in the presence of barcoded gel beads and oil to create GEMs (Gel Bead in EMulsion). Up to 8 samples can be run simultaneously per chip.
As many as 10,000 cells per sample are encapsulated in nano-liter scale GEMs. Final amplification and library construction is performed in bulk after GEMs are broken. Resulting libraries are compatible with Illumina sequencing platforms.
Application
The following applications are available:
- 3' Gene Expression
- Targeted gene expression (custom or panels)
- Assay for chromatin accessibility (ATAC Seq)
- Immune profiling of B and T cell receptors and 5' gene expression
- Multiomic (Gene Expression + ATAC)
In addition, the following applications can be paired with gene expression assays/immune profiling:
- Identification of CRISPR perturbations
- Antibody-based feature barcoding can be used to quantify the levels of cell surface proteins
Expertise & Services
The Genomics Core provides advice on initial experimental planning and costs for grant proposals. Researchers interested in using the 10X platform are encouraged to contact the Genomics Core to discuss prospective projects
A full service is provided, from library generation to sequencing, across the application range.
Contact
Ms Alison Murphy
T: (+353-1) 716 6955
E: alison.murphy@ucd.ie
Agilent Bionalayser
The Agilent 2100 Bioanalyzer is a chip based automated electrophoresis platform for sizing, quantification and quality control of RNA and DNA. It utilises microchannel electrophoretic separation to produce a rapid and sensitive measure of nucleic acid quality and size. The Bioanalyzer software creates a graph called an electropherogram, which diagrams fluorescence over time as molecules are pulsed through the separation channel. An essential tool for quality assessment of RNA, DNA and NGS libraries.
Further information can be found here, Agilent Bioanalyser
Applications
RNA Nano chips and High Sensitivity DNA Chips are in stock within the Facility.
Access and Services
Researchers are trained to become independent users of the system, with ongoing technical support available as required.
Bioanalyser booking is via our online booking system, Clustermarket. New users can register for access and training by following the link Bioanalyser Booking & Registration
Agilent Tapestation
The Agilent 4200 Tapestation is a fully automated electrophoresis tool for DNA, RNA and NGS Library quality control. It operates in low to high throughput (96 well) mode, utilising ready to use Screentapes.
Access and Services
Researchers are trained to become independent users of the system, with ongoing technical support available as required.
Screentapes are not currently stocked within the Facility. The complete range of available Screentape Assays can be viewed via the following link: Tapestation and reagents.
Contact
Ms Alison Murphy
T: (+353-1) 716 6955
E: alison.murphy@ucd.ie
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