NGS services utilize an Illumina NovaSeq X Plus for low-cost, high-throughput sequencing and an iSeq 100 for quality control and validation. Sequencing services are supported by expertise in manual library prep and automated library prep on a PerkinElmer Zephyr G3 NGS and Hamilton Vantage.
For RNA-seq, Roche Kapa RNA Hyper and Illumina TruSeq workflows support a range of input amounts.
DNA-seq libraries for fragmented DNA submissions like ChIP are supported by Kapa DNA Hyper and DNA Evo. For metagenomics and whole genome studies enzymatic fragmentation workflows are available with additional sample cleanup to provide efficient library conversion.
Hybridization capture workflows for whole exome sequencing and targeted panels are supported upon request.
The OGSR also provides a sequencing only service, where users can submit their own NGS libraries or library pools for sequencing following in-house quantification and fragment analysis.
The OGSR also provides Sylvester members with access and support for use of long-read sequencing technologies located in the HIHG GCT, including the Oxford Nanopore Technologies PromethION and the PacBio Revio. Applications include direct methylation sequencing, full-length transcript sequencing and structural variant analysis.
Single-Cell Genomics
Single-cell and single-nuclei gene expression profiling is run on a 10x Genomics Chromium single cell controller supported by sample QC on a Nexcelom K2 imaging cell counter. Services are available for all Chromium protocols including gene expression profiling, immune profiling (V(D)J sequencing), feature barcoding (CITE-seq), with submission supported for both fresh and fixed samples.
An S2 Genomics Singulator 200 is available for walk-up service for tissue dissociation and nuclei prep. The platform has preconfigured protocols for many applications that can be optimized for specific tissues.
A dual rotor Miltenyi GentleMACs dissociator and manual Miltenyi MACS separator are also available for use in investigator labs. Applications include preparation of cell suspensions and dead cell removal.
Spatial Multiomics
In concert with histopathology services delivered by the Cancer Modelling Shared Resource (CMSR), the OGSR supports multiple spatial multiomics platforms for interrogating gene and protein expression.
The 10X Genomics Visium platform is a data-driven approach that captures gene expression profiles using spatially addressed oligo spots. Our workflows support FFPE sections and probe-sets for human or mouse whole transcriptome studies.
In-situ spatial molecular imaging is supported by the Bruker CosMx for data-driven studies with signatures partitioned into cellular bins using bioinformatic segmentation. This platform uses panels of up to 6,000 transcripts or 64 proteins and provides sub-cellular resolution. Cell segmentation is enabled by curated panels of cell surface markers and nuclear stains. Applications include cell atlasing, neighborhood and proximity analysis and receptor:ligand expression studies.
High resolution regional sampling, similar to laser capture microdissection, is available using the Bruker GeoMx digital spatial profiler. This hypothesis-driven approach supports whole transcriptome studies of human and mouse tissues along with panels of up to 570 validated antibodies. Areas of interest for sampling can be manually selected by investigators or automated using counter stains.
Gene Expression and Molecular Quantification Assays
The Bruker nCounter® Pro platform generates gene expression data using panels of up to 800 targets using solution-phase hybridization, immobilization and barcode counting. Curated panels are available for areas of cancer research and the technology works well with RNA from FFPE.
Digital PCR (dPCR) services are available using a QIAgen QIAcuity One. dPCR is suited to applications such as genotyping, viral load counting and transcript quantification. Assays are typically run using hydrolysis probes (Taqman) and can be multiplexed using three channel detection. Validated hydrolysis qPCR assays can usually be transitioned easily to dPCR.
Nucleic Acid Extraction, Quantification, and Quality Control (QC)
RNA and DNA extraction services are available for cells, tissues, biofluids, and FFPE. Standard extraction procedures run on a Thermo KingFisher Apex mag-bead extractor with GentleMACS homogenization. Manual extractions are also available for complex workflows.
Sample quantification is available using Qubit 3 and Qubit Flex or micro-volume spectrophotometry using NanoDrop 8000.
Fragment analysis, including services to determine total RNA and gDNA integrity, are available using Agilent 2100, 5200 and Femto Pulse systems. All of which are capable of analysis of low or standard input samples (~0.2 - 100 ng) with fragment resolution supported from <20bp to 165Kb across the three platforms.