Applications

The facility supports a diverse range of applications, such as Oxford Nanopore long-read sequencing, whole genome sequencing (de novo and resequencing), de novo whole transcriptome sequencing and RNAseq for gene expression, whole exome sequencing, microbiome and microbial community profiling, metagenomics of both culturable and unculturable organisms, single cell WGS, RNAseq and ATACseq, and targetted resequencing for genotyping, haplotyping, rare variant detection and structural variation detection and of the methylome and regulome (ChIPseq).

CGEBM houses a dedicated, purpose built single cell genomics lab for RNAseq, ATACseq and CNV detection at single cell resolution, and a and low copy DNA lab for anthropological and archaeological studies into evolution and environmental change. Additionally, this facility is used to enable sample preparation of other low copy DNA projects. Development and validation of aDNA techniques and technologies is expected to be directly applicable to the vast array of archived, low quality clinical specimens (e.g. FFPE) available to researchers for clinical and translational studies at Aberdeen.

 

Capability

Projects include microbial (prokaryotic and eukaryotic), plant and animal species that have genomes of distinct size, structure and annotation level, either with or without a reference genome.

Sample types include nucleic acid polymers extracted from fresh, frozen and FFPE cells, tissues and organisms, as well as ancient DNA from archeological skeletons, other human remains and archived tissues and herbarium samples.

Our Illumina MiSeq, Illumina NextSeq 500 and Ion Torrent Proton NGS systems are compatible with bar-coding for multiplexing of samples to ensure cost effectiveness in both lower samples sizes with higher read depths and high sample sizes at lower read depths. We are able to perform single end reads, paired end reads and mate-pair sequencing as required to facilitate an optimal design for each application. Nanopore long read sequencing provides long sequencing reads as well as direct DNA/RNA sequencing for applications such as improved de novo assemblies, detection of structural variants, phasing, detection of fusion transcripts, splice variant analysis, DNA or RNA epigenetics, real-time metagenomics.

Support

The facility has dedicated technical support, specialised expertise and equipment to provide a comprehensive service from high throughput DNA extraction and library preparation, including QC and normalisation, through to automated template preparation (clonal amplification) and massively parallel sequencing.

The CGEBM bioinformatics, alongside biostatistics, biocomputing and data management services provide capacity for assembly, interpretation, storage and sharing of the complex NGS datasets that are generated.