Professor Brendan Loftus directs the UCD Conway Genomics Core, which has a range of facilities for next-generation sequencing, real-time PCR and microarray analysis as well as offering custom bioinformatics analysis. The Genomics Core has been offering genomics solutions to academic and commercial customers for more than 10 years in a customisable range of services for each stage of the research pathway, from experimental design and strategy to final publication.

These core technologies have been leveraged in a wide range of large human disease studies; on a variety of microbial pathogens either to measure response or following an outbreak; and even on ancient DNA extracted from fossil specimens.

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Affymetrix Microarray
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The Affymetrix GeneChip microarray platform consists of high-density microarrays and tools to process and analyse them, including standardised assays and reagents, instrumentation, and data management and analysis tools. GeneChip microarrays consist of small DNA fragments known as probes, chemically synthesised at specific... Show more »

The Affymetrix GeneChip microarray platform consists of high-density microarrays and tools to process and analyse them, including standardised assays and reagents, instrumentation, and data management and analysis tools. GeneChip microarrays consist of small DNA fragments known as probes, chemically synthesised at specific locations on a coated quartz surface. The precise location where each probe is synthesised is called a feature, and millions of features can be contained on one array.

Applications
By extracting and labelling nucleic acids from experimental samples and then hybridising those prepared samples to the array, the amount of label can be monitored at each feature, enabling a wide range of applications on a whole-genome scale including gene- and exon-level expression analysis, novel transcript delivery, genotyping and resequencing. Microarray analysis can also be combined with chromatin immunoprecipitation to perform genome-wide identification of transcription factors and their respective binding sites.


Instrumentation:
- GeneChip 3000 7G scanner
- Automated fluidics 450 station
- Hybridisation oven
- GeneChip workstation with AGCC Software
- Agilent bioanalyser
- Nanodrop spectrophotometer


Expertise & Services:
- Initial meeting to discuss experimental design and strategy
- Advice on sample preparation and provision of protocols
- Optional sample preparation and labelling service
- Quality assessment of total RNA and cRNA
- Array hybridisation, washing, staining & scanning
- Assessment & monitoring of array quality
- Primary data analysis, provision of QC report and raw data files

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Affymetrix
ChIP-Seq Data Analysis
Chromatin immunoprecipitation-sequencing data analysis
Price on request

Modern high throughput technologies have changed the way many experiments are designed and interpreted. Understanding the technologies is paramount in the design of effective experimental strategies. When high-throughput raw data are generated, specialist analytical techniques must be applied to produce valid results for... Show more »

Modern high throughput technologies have changed the way many experiments are designed and interpreted. Understanding the technologies is paramount in the design of effective experimental strategies. When high-throughput raw data are generated, specialist analytical techniques must be applied to produce valid results for subsequent biological interpretation.

UCD Conway Institute provides the opportunity for 'wet-lab' biologists to interact with bioinformaticians at various points along the pathway from an experimental idea to final publication.

Expertise & Service:
Bioinformatics support is available in the Genomics Core facility. We have a wealth of experience in many facets of data handling for genomics and transcriptomics, extending to over 20 years of DNA sequencing and analysis. Genomics Core facility analysis is provided in the following areas:
- mRNA seq
- ChIP seq
- Prokaryotic genome sequencing
- Affymetrix gene expression arrays

Quality control and primary analysis of the data is provided for all projects. Custom analysis including functional mapping and pathway analysis are also available.

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Illumina Sequencing
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The Illumina sequencing platform is used for a variety of genomics/transcriptomics and epigenomics studies. The system utilises reversible terminator chemistry, to deliver high levels of accuracy, cost effectiveness and throughput. Users include research centres, pharmaceutical companies, academic institutions, clinical research... Show more »

The Illumina sequencing platform is used for a variety of genomics/transcriptomics and epigenomics studies. The system utilises reversible terminator chemistry, to deliver high levels of accuracy, cost effectiveness and throughput. Users include research centres, pharmaceutical companies, academic institutions, clinical research organisations and biotechnology companies.

Applications:
The platform supports a diverse range of applications including RNA-Seq, digital gene expression, whole genome and candidate region sequencing, DNA-protein interaction profiling and small RNA identification.


Expertise & Services:
We provide a range of technical services and expertise in this area including:
- Discussions surrounding, suitability of the platform, experimental design and strategy
- Advice on sample preparation and provision of protocols
- Sample QC, library preparation, cluster generation and sequencing
- Preliminary data analysis to generate aligned sequence, if genome is known
- Provision of FASTA Q and/or other data files for further analysis
- Downstream bioinformatics analysis, on request

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miRNA-Sequencing Data Analysis
Price on request

Modern high throughput technologies have changed the way many experiments are designed and interpreted. Understanding the technologies is paramount in the design of effective experimental strategies. When high-throughput raw data are generated, specialist analytical techniques must be applied to produce valid results for... Show more »

Modern high throughput technologies have changed the way many experiments are designed and interpreted. Understanding the technologies is paramount in the design of effective experimental strategies. When high-throughput raw data are generated, specialist analytical techniques must be applied to produce valid results for subsequent biological interpretation.

UCD Conway Institute provides the opportunity for 'wet-lab' biologists to interact with bioinformaticians at various points along the pathway from an experimental idea to final publication.

Expertise & Service:
Bioinformatics support is available in the Genomics Core facility. We have a wealth of experience in many facets of data handling for genomics and transcriptomics, extending to over 20 years of DNA sequencing and analysis. Genomics Core facility analysis is provided in the following areas:
- mRNA seq
- ChIP seq
- Prokaryotic genome sequencing
- Affymetrix gene expression arrays

Quality control and primary analysis of the data is provided for all projects. Custom analysis including functional mapping and pathway analysis are also available.

« Show less
qPCR
Quantitative PCR
Price on request

Real-Time PCR is a powerful and sensitive technique for detection and quantification of specific nucleic acid sequences. It monitors the polymerase chain reaction (PCR) as it occurs and characterises samples at the point of initial amplification of PCR product rather than the amount accumulated after a fixed number of cycles. The... Show more »

Real-Time PCR is a powerful and sensitive technique for detection and quantification of specific nucleic acid sequences. It monitors the polymerase chain reaction (PCR) as it occurs and characterises samples at the point of initial amplification of PCR product rather than the amount accumulated after a fixed number of cycles. The higher the starting copy number of target sequence, the sooner its PCR product is detected.

Application:
Both relative and absolute quantitative analysis may be investigated. Relative quantification provides comparative measurement of target across a set of biological samples and is used in applications such as gene expression profiling, microRNA and siRNA studies. Absolute quantification assigns values of target to samples from external standards and examples include copy number determination and viral load measurement. This technology may also be used in conjunction with end-point reads for allelic discrimination or SNP detection.


Instrumentation:
Two ABI 7900HT Sequence Detection Systems are in operation in this facility comprising::
- Primer Express Software v2.0 (primer and probe assay design)
- Interchangeable thermal cycling blocks (Fast and Standard)
- Laser and CCD camera detector (fluorescence induction and data collection)
- Sequence Detection Software v2.4 (instrument operation and data analysis)
- Samples are run on 96- and 384-well plates or microfluidic cards with Taqman probe or Sybr Green based fluorescent assays. These assays are designed and optimised or purchased commercially in pre-optimised single tubes or array formats for higher throughput experiments.


Expertise & Services:
The Real-Time PCR core facility provides a range of technical services to researchers including:
- Consultation on experimental design
- Assay design and ordering
- Training on sample set-up, instrumentation and data interpretation
- Sample running service, if required
- Results analysis

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DNA Sequencing
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DNA Microarrays
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Biology
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Sequencing Data Analysis
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Nucleic Acid Analysis
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Nucleic Acid Data Analysis
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Next Generation Sequencing (NGS)
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PCR
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DNA
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Biochemistry & Molecular Biology
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Nucleic Acid Services
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