UF Surgery Genomics Core

Located on the fourth floor of the ARB, the UF Surgery Genomics Core Facility offers a wide range of services to all investigators in the Surgery Department at UF. We focus on single-cell genomics and high-throughput sequencing services using Illumina NextSeq 1000 and the 10x Genomics Chromium X.  The Genomics Core provides a centralized resource working to take the difficulty out of high throughput (Next Generation) sequencing projects for both novice and experienced users. To accomplish this, we provide assistance in design and data analysis. We strive to service our research community in a cost-effective and efficient manner to enable them to conduct the best research possible.

Grant Resource Info 

Surgery Department Genomics Core. The UF Surgery Department Genomics Core includes an Illumina NextSeq 1000 which enables effective throughput next-generation sequencing (NGS) with scaling to suit virtually any study need and provides our investigators with the throughput, speed, and flexibility. The UF ICBR also has available an Illumina NovaSeq 6000 high-throughput sequencer for additional applications. There is a droplet-based single-cell system 10X Genomics Chromium X which allows researchers to choose single-cell sequencing methods as needed, such as RNA-Seq, ATAC-Seq, TCR/BCR repertoire sequencing, etc. There is instrumentation to support sequencing prep (QIAGEN automated QIAcube Connect), DNA and RNA Quality control (Agilent 2100 Bioanalyzer, Qubit4 Fluorometer; Agilent Stratagene MX 3005P real-time PCR Analyzer), and library construction (X2 BioRad T100 thermal cyclers, Tecan Evo automated liquid handler ). Additionally, the core includes both a NanoString Flex nCounter Prep Station and NanoString nCounter Digital Analyzer for both initial discovery and validation of sequencing data, as well as targeted transcriptomics. The core includes a dedicated biologic scientist with expertise in library creation, sequencing, and initial bioinformatic analysis using Illumina DRAGEN and 10x Genomics Cell Ranger software suites. Dedicated pipelines for data transformation, alignment, and trimming are assisted by our departmental bioinformatician and statistician.

Director: Guoshuai Cai, PhD

Lead Scientist: Marvin Dirain, MS

The following outlines expectations for workflow when using the Core.

PI responsibilities – develop and validate protocols for: single cell isolation, high-quality DNA/RNA isolation, single nuclei isolation. Determine methodology desired (bulk RNA-seq, single-cell RNA-seq, single-cell ATAQ-seq, CITE-Seq, etc). Provide reagents for library preparation, sequencing, etc.

Core responsibilities – library preparation from RNA/bar-coded samples, sequencing samples, provide consultation on best methodologies to be utilized, advise on data analysis methods

Request a consultation (Smart Form TBA): PI, Study Overview,  Type of Services Requested, # of Samples, Grant Deadline/Agency if Applicable, Anticipated start date, Is consult needed on best approach/methodology?

UF Surgery Genomics Core

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