USF Genomics

USF Genomics Program Services

The USF Genomics Program has the capability to assist with both sample sequencing and computational analysis for research projects at USF.


  • USF Genomics Program Sequencing Core

    The USF Genomics Program Sequencing Core is a NextGen Sequencing laboratory facility which consolidates resources and expertise to provide genomics laboratory training from the Library preparation to Next Generation Sequencing. The core offers assistance with experimental design, trouble shooting, and data analysis. Certified users may reserve time in the USF Genomics Equipment Core for library prep and sequencing. Completion of the USF Genomics RNAseq Laboratory Training is required to become a certified user of the Core. The following services are available for USF users:

     Instrumentations

    Equipment for NextGen Sequencing

    • Illumina – NextSeq 2000 ·     
    • Illumina - MiSeq System · 
    • Illumina – NovaSeq (Service provides with a partnership) ·        
    • 10x Genomics- Chromium Controller Single Cell Instrument

    Instrumentation for library-prep and quality assurance

    • Agilent - TapeStation 2200, TapeStation 4200 (DNA and RNA quality assessment) ·       
    • Invitrogen Qubit 4.0 fluorometer (DNA and RNA sample quantification) ·        
    • Roche - LightCycler 96 Real-time PCR Instrument (DNA library quantification) ·        
    • Covaris - M220 Focused Sonicator (DNA fragmentation) ·        
    • Nexcelom - Cellometer K2 Image Cytometer ·        
    • Eppendorf - epMotion, 5075tc NGS & Automation System

    Sequencing Services Overview 

    General Sample/Library QC Services

    • Qubit ·        
    • TapeStation ·        
    • General library QC ·        
    • qPCR - Library Quantification ·        
    • Covaris - DNA Fragmentation ·        
    • Cellometer K2 - Cell Counting

    Library Construction Services

    • DNA Library Prep construction (WGS, shotgun-genome, 16S metagenomics) ·        
    • RNAseq Library Prep - Illumina Truseq mRNA library construction ·        
    • miRNA library construction ·        
    • ChIP-Seq library construction ·        
    • Methylation library construction  ·        
    • Custom Library Prep ·        
    • Automation Library Prep

    Single-Cell Library Preparation (10x Genomics)

    • Chromium Single-Cell Library Construction (3'/5'/ATAC-seq) ·      
    • Single-Cell Immune Profiling - V(D)J with 5' GE  ·        
    • Single-Cell Multiome ATAC + GE

    Illumina Sequencing Services

    • Miseq v3 - 25 M reads (150, 600 cycles) ·        
    • Miseq v2 - 15 M reads (50, 300, 500 cycles) ·        
    • Miseq Nano v2 - 1 M reads (300 cycles) ·        
    • Miseq Micro v2 - 4 M reads (300 cycles) ·        
    • NextSeq 2000 P1 - 100 M reads (300 cycles) ·        
    • NextSeq 2000 P2 - 400 M reads (100, 200, 300 cycles) ·        
    • NextSeq 2000 P3 - 1200 M Reads (50, 100, 200, 300 cycles) ·        
    • NovaSeq 6000 (SP, S1, S2, S4, Service provides with a partnership)

    Consultation Services

    • Project Consultation (letter of support, methods, experimental design, cost estimate) ·
    • Sequencing Instrument Assistance ·        
    • Library Preparation Assistance ·        
    • Quality Check - Sample and Library QC ·        
    • Sequencing Method Development Work - R & D ·        
    • Troubleshooting Assistance ·        
    • Basic Data Analysis Assistance ·        
    • Grant Proposal & Manuscript Preparation Work ·        
    • Genomics Laboratory Training

    More Information

    USF Genomics Core Policies and Procedures

    USF Genomics Core Service Agreement

    Sample Submission Sheet

    USF Genomics Core Rate Sheet

    RNAseq Protocols

     

    Questions regarding the USF Genomics Equipment Core can be sent to genomics@usf.edu. At this time, core services are now open to users outside of USF.

  • USF Genomics Program Computational Core

    The USF Genomics Hub is the computational branch of the USF Genomics Core. The Hub consists of computational biology consultants for genomics research projects. These consultants run Mac, Linux and Windows workstations and have access to USF’s High-Performance Computing (HPC) cluster and a variety of both proprietary and open-source, command-line based analysis software. Data analyzed by the Hub are securely stored on a new HIPAA-compliant component of USF’s HPC cluster. HPC infrastructure and hardware supporting USF Genomics and the USF Genomics Core Facility is managed by the USF Department of Research Computing.

    The members of the USF Genomics Hub also are instructors for the USF Genomics RNAseq Data Analysis Training. This training reviews theoretical and practical concepts related to RNA sequencing analysis, enabling them to perform these analyses independently.

    To place requests for computational assistance from the USF Genomics Program, please submit queries through the link below. After submitting a request, a member of the Hub will reach out to set up a consultation time.

    USF Genomics Computational Inquiry Form

    For more information, contact genomics@usf.edu or visit the USF Omics Hub GitHub website.

  • Access to iLab (How to submit a Work Request)

    The USF Genomics Core now uses the iLab operations software for all project-specific communications (quotes, service requests, equipment reservations). In order to use iLab, users must create a free account with their USF email.

    FirstTime iLab User Guide

    iLabUser Instructions

    Specifics on how to create an account and submit a request may be found in iLab User Instructions.

    USF Genomics Program Sequencing Core Homepage: https://my.ilabsolutions.com/service_center/show_external/5175.

    If you have an inquiry about general pricing, see the "USFGenomics Core Rate Sheet". 

  • More Information

    The USF Genomics Program has assembled resources for PI's at USF to use when applying for grants. The following document includes the resources and facilities available through the USF Genomics Program:

    USF Genomics Facilities and Resources

  • Need Help?

    For general questions, assistance with proposals, etc., submit your question/request with the  USF Genomics Program Core Request Form or email genomics@usf.edu.