DNA and RNA sequencing in recent years have taken big leaps in terms of accuracy, length, and accessibility. In keeping with these trends, SKAN Research Trust has invested heavily in establishing a sequencing facility that caters to all three generations of sequencing instruments.
Applied Biosystems SeqStudio 8 Flex
Our SeqStudio Flex 8 is a first-generation Sanger sequencing platform with cloud connectivity and run prioritization capabilities. It uses Bigdye termination-based sequencing chemistry to provide >800bp single primer read length for applications such as plasmid sequencing to verify reading frames and SNPs, and it is also used for routine amplicon sequencing for applications such as microbial identification and variant validation.
Illumina NextSeq 2000
A high level of multiplexing is achieved on our second-generation sequencing platform, the Illumina NextSeq 2000, which currently runs XLEAP-SBS (sequencing-by-synthesis) chemistry, delivering a maximum output of up to 540 Gb with a high proportion of bases at Q40 or higher quality scores, all within a compact instrument footprint. The platform also supports an onboard DRAGEN server to facilitate real-time data analysis and enables several compute-intensive bioinformatics pipelines. This allows researchers at SKAN to perform targeted and untargeted metagenomics, exome sequencing, RNA sequencing, exploratory proteogenomics, and single-cell sequencing at scale.
Oxford Nanopore Technologies MinION
The sequencing facility also has long read third generation sequencers from Oxford Nanopore Technology to achieve multi-kilobase read lengths with the ability to complete native DNA and RNA sequencing. The nanopore-based sequencing approach directly detects changes in ionic current as nucleic acids pass through engineered nanopores, allowing sequencing without the need for amplification or fluorescent labeling. Further, the platform also supports our efforts to augment untargeted metagenomics with long reads to carry out genome-resolved metagenomics studies on gut microbiome samples.
Together, these platforms form a key part of the multi-omics ambition of SKAN Research Trust to generate datasets supporting investigations in various research domains and answering key questions related to ageing and longevity.
Single-Cell Sequencing Technology – 10x Genomics Chromium X
The 10x Genomics Chromium X platform represents a cutting-edge platform driving next-generation single-cell discovery at SKAN Research Trust. As a state-of-the-art high-throughput single-cell analysis system, Chromium X enables comprehensive characterization of cellular heterogeneity at unprecedented resolution, empowering researchers to dissect complex biological systems at the level of individual cells.
The platform supports a wide range of single-cell and single-nucleus applications, including:
- Single-cell RNA sequencing
- Single-nucleus RNA sequencing
- Single-cell ATAC sequencing
- Single Cell Multiome analysis
- Immune profiling and V(D)J repertoire analysis
The Chromium X system allows the processing of both fresh and cryopreserved samples, as well as fixed tissues and nuclei isolated from human and murine specimens. By enabling the analysis of thousands to hundreds of thousands of individual cells in a single experiment, the platform provides unparalleled insights into cellular diversity, lineage relationships, developmental trajectories, and disease-associated molecular programs.
At SKAN Research Trust, we plan to extensively utilize the Chromium X platform to investigate fundamental and translational questions across multiple research domains, including hematopoietic stem cell biology, leukemia and bone marrow microenvironment research, neurobiology, aging, regenerative medicine, and induced pluripotent stem cell (iPSC) biology. The integration of single-cell transcriptomics, epigenomics, and multi-omics technologies with our advanced flow cytometry, imaging, and next-generation sequencing capabilities substantially enhances the depth and impact of our research programs.