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.
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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
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.
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USF Genomics Program Computational Core
The USF Genomics Computational Core is the computational branch of the USF Genomics Core. The computational core provides consulting and data analysis of RNA and DNA sequencing, proteomics, metagenomics, database management, and pipeline design and development. The consultants have access to USF’s High-Performance Computing (HPC) cluster and a variety of open-source software and proprietary to analyze data. The analyzed data are securely stored on 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 following services are available for USF users:
Computational Core Service Overview
General Hourly-Based Services
- Computational Core Consultation
- Data Cleaning, Releasing, Submission, Transfer
- Sequence Alignment and Mapping
- Sequencing Data Quality Control
- Functional Annotation
- Pathway Reconstruction
- Project-based Method/Study Design
- Application Development
- Database Design
- Management Manuscript/Report Writing
General Project-Based Services
- Bulk RNAseq Analysis
- Chip-seq Analysis
- DNA Methylation Analysis
- DNAseq Analysis
- Metagenomics Analysis
- Proteomics data analysis
- Metabolomics/Lipidomics data analysis
- Single-cell data analysis
Work requests for computational services must be submitted through iLab.
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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.
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".
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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:
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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.