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Onco-Genomics Services

Next Generation Sequencing (NGS)

  • NGS services utilize a NovaSeq 6000 for low cost high capacity sequencing, a NextSeq 500 for smaller rapid runs 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.

  • For ribo-depleted RNA-seq studies Nugen SOLO Ovation library prep support inputs <1-10ng. Kapa RNA Hyper and Illumina TruSeq workflows support standard input submissions.

  • DNA-seq libraries for fragmented DNA submissions like ChIP are supported by Kapa DNA Hyper and Swift 2S protocols. For metagenomics and whole genome studies Kapa DNA HyperPlus workflows are available with additional sample cleanup and fragmentation optimized on a per project basis to provide efficient library conversion. Bulk immune profiling is provided using ArcherDx Immunoverse reagents. SARS-CoV-2 genome sequencing is supported by ARTIC amplicon sequencing (Swift, NEB) and hybridization capture (Twist, Roche).

  • Aside from in-house library prep, the OGSR provides a sequencing only NGS service, where users can provide their own NGS libraries or library pools for sequencing.

Single Cell Genomics

  • Gene expression multi-omics studies are 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 10X Genomics protocols including 3’ and 5’ gene expression and T cell and B cell receptor sequencing and “feature barcoding” applications including cell surface antibodies and antigens.

  • DNA sequencing multi-omics studies are run on Mission Bio Tapestri with many off-the-shelf panels for cancer driver mutations and applications for CNV. Workflows for the incorporation of cell surface antibodies are also available.

  • The OGSR also has access to a Fluidigm C1 system via the Miami Center for AIDS Research (CFAR).

  • A dual rotor Miltenyi GentleMACS tissue dissociator is available to loan to assist with sample prep for single cell studies.

Gene Expression and Molecular Quantification Assays

  • The nanoString nCounter® platform is a complete solution for detecting and counting large sets of molecules using solution-phase hybridization, immobilization and fluorescence scanning. Digital molecular barcoding enables researchers to directly count the number of target transcripts in each sample. nanoString barcodes enable multiplexing and can quantify up to 800 targets for gene expression or miRNA analysis. The OGSR runs an nCounter Gen2 Analysis System designed for core facilities and can operate at a throughput of 24 samples per day.

  • We can provide droplet digital (ddPCR) services on a BioRad QX200 system. ddPCR is particularly suitable for applications such as genotyping or validating somatic mutations, viral load counting and absolute transcript quantification. Assays are typically run using hydrolysis probes (Taqman) and can be multiplexed using dual channel detection. Validated hydrolysis qPCR assays can usually be transitioned easily to ddPCR.

Nucleic Acid Extraction, Quantification, and Quality Control (QC)

  • RNA and DNA extraction services are available for cells, tissues, biofluids, and FFPE. Homogenization can be carried out using cryo-fractionation (Covaris CryoPrep) or grinding (Miltenyi GentleMACS) in sealed single-use vessels. Our standard extraction procedures use Qiagen kits. Other commercial protocols may be available upon request. Phenol-Chloroform extraction is not available.

  • Sample quantification is available using Qubit or Quant-iT dye-based systems or micro-volume spectrophotometry using NanoDrop.

  • Fragment analysis, including services to determine RNA integrity, are available using Agilent 2100, or 5200 systems. Both systems are capable of analysis of low or standard input RNA or DNA samples (~1 - 100 ng) with fragment sizes up to about 6Kb.