NextGen Sequencing

 The NextGen DNA Sequencing Core provides high quality, massively parallel, high-throughput sequencing services covering a broad range of applications for biological research including transcriptome analysis, targeted genome and variant analysis, microbiome analysis, epigenetics, and de novo genome assembly. The Core utilizes the most current instrumentation, including the PacBio SEQUEL, and Illumina MiSeq, NextSeq, and HiSeq3000 platforms. Library construction services from many applications are available for all platforms. Customers are encouraged to consult with core staff for the purpose of selecting the best experimental approach and instrument platform for addressing specific research questions.

The NGS-SR, a partnership between the UFHCC and the UF Interdisciplinary Center for Biotechnology Research (ICBR), is located within the Cancer Genetics Research Complex (CGRC) and provides UFHCC members access to state-of-the-art instrumentation and scientific and technical expertise for conducting impactful genomic-based research studies in support of the strategic aims of basic, translational and clinical cancer research activities.

Comprehensive NGS services include DNA structural and gene variant analysis, microbiome and metagenome analysis, RNA-Seq, chromatin modifications and epigenetics. The NGS-SR performs DNA library preparation and quality assessment, with the majority of sequencing analysis using the Illumina short-read DNA sequencing platform. For more complex applications requiring longer single molecule read lengths like RNA splicing analysis, the PacBio SEQUEL instrument is available. Researchers requiring access to single-cell analysis can utilize NGS-SR staff expertise in the 10X Genomics Chromium platform troubleshooting.

The NGS-SR works closely with the UFHCC BQS-SR and ICBR Bioinformatics to streamline handoff of raw sequencing data for downstream analysis. The working hours of the NGS-SR are 8 a.m. to 6 p.m. Monday through Friday. Researchers must obtain CrossLab user accounts to access NGS services. UFHCC members benefit from priority access to all services. All data generated are transferred directly from the instruments to ICBR’s local secure storage environment and simultaneously upload to Illumina’s BaseSpace Sequence Hub (a cloud-based genomics computing and storage platform) allowing ICBR to offer a wider array of analysis workflows, and QA/QC for Illumina data. Conversely, PacBio data is analyzed locally on PacBio’s SMRT Link, a system accessible only to ICBR. Subsequently, datasets are compiled into a unified deliverable and sent to customers using Globus, a grid-FTP data transfer platform that allows delivery of very large datasets in a rapid fashion while safeguarding data security and integrity) or hardware encrypted hard drives.