Genomics
Providing Next Generation Sequencing services for the research community.

Genomic sequencing

Welcome to the Genomics Core at The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology!

Our goal is to provide investigators in our Jupiter, Florida campus as well as external investigators the latest technologies in Next Generation Sequencing (NGS).

We strive to provide the best service possible to our research community and encourage all investigators interested in incorporating sequencing analysis to their projects to contact us. The Genomics Core uses NGS platforms to address a wide variety of research needs. Consultation on sample preparation and procedures is also provided and highly recommended before starting your projects.


Working With Us

The Genomics Core supports a wide array of experimental approaches including:

  • Whole transcriptome sequencing (polyA enrichment or rRNA-depletion)
  • Small RNA sequencing
  • Ribosome profiling
  • Ultra-low input RNA sequencing
  • Single cell transcriptome profiling with 10X chromium (for 1000 – 20,000 cell capture) or for individual single-cells using the SMART-seq approach
  • ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing)
  • Methyl-Seq: Whole genome methylation analysis with Enzymatic Methyl-Seq
  • Regulatory DNA or RNA interactions with proteins (RIP-seq, ChIP-seq) analysis
  • Splice variant quantification
  • For more information, please contact our staff

All work performed by The Wertheim UF Scripps Institute Genomics Core Facility that supported your research should be acknowledged in all presentations, posters, papers and scholarly articles. Your acknowledgement provides an important visible measure of the impact of our facility and is essential for our continued funding and operation. Please at a minimum acknowledge the Genomics Core in your publications and if a staff member made a significant intellectual contribution, please consider co-authorship. Suggested text for citation: Library preparation and sequencing (or other analyses, i.e. bioanalyzer assessment, sonication, qRT-PCR) was performed at The Wertheim UF Scripps Institute Genomics Core. Please see the ABRF guidelines for authorship for personnel working in core facilities: https://abrf.org/authorship-guidelines


Our Equipment

Illumina Next Generation Sequencing Platforms

Please contact Core staff for questions regarding sample preparation and concentration.
  • NextSeq 2000: The NextSeq 2000 fast sample-to-results workflow enables rapid sequencing of exomes, whole genomes, and transcriptomes in a single run. The NextSeq 2000 supports a broad range of sequencing applications and offers tunable read length (from 50 to 600bp) and multiple output configurations providing up to 1.2 billion reads for pair-end sequencing runs. Additionally, the NextSeq 2000 is fully integrated with BaseSpace to simplify data sharing in the cloud. 
  • MiSeq: The MiSeq can provide up to 25 M reads with 2x300bp read chemistry, allowing a broad variety of applications such as amplicon sequencing, targeted resequencing, 16S metagenomics, small RNA sequencing, and small genome sequencing. The MiSeq has on-board data analysis capability and full integration with BaseSpace.

10x Genomics Chromium X

The Chromium X instrument provides access to single cell sequencing experiments based on the industry leading 10x Genomics technology. It is compatible with all currently available 10x Genomics kits for single cell gene expression, chromatin accessibility, and immune profiling. Depending on the assay used, it can process hundreds to hundreds of thousands of cells per run, increasing the experimental flexibility over the previous generation Chromium controller.

10x Genomics library preparations are carried out by the Genomics Core personnel. Please contact us before starting any single cell experiments, as most of the assays require immediate processing, which necessitate close coordination to ensure personnel availability.

Agilent 2100 Bioanalyzer and 4200 TapeStation

The Genomics Core offers analysis of nucleic acid samples (both RNA and DNA) using the Agilent 2100 Bioanalyzer and 4200 Tapestation. Both systems assess sizing, quantity and quality of DNA and RNA, providing high quality data. The Bioanalyzer RNA kits with the patented RNA Integrity Number (RIN) are industry standard for RNA quality assessment, allowing reliable and precise integrity checks and sample quantitation before any RNA-dependent application. Only as low as 100 pg of total RNA is required for analysis. The resolution of small nucleic acids (size range of 6 to 150 nt) can also be achieved by utilizing the small RNA kit. The DNA kits are ideal for automated sizing and quantitation of PCR fragments, restriction digests or fragmented DNA, with a sensitivity as low as 5 pg/ul.  

The user provides samples at the required concentration and the Genomics Core personnel will run the samples on the bioanalyzer chip and email the results. Please contact us for questions regarding sample preparation and concentration.

Covaris S220 sonicator

The core houses the Covaris S220, a focused ultrasonicator based on Covaris’ Adaptive Focused Acoustic technology, recognized as the gold standard in DNA, RNA, or chromatin ultrasonic shearing. The S220 can be used in upstream processing of variety of samples in preparation for sequencing experiments.

To reserve time on the instrument, please sign up using the calendar in our iLab system. Charges are on a per-hour basis. Cancellations should be performed 24 hours prior to usage. Otherwise, the user will be charged for the number of hours reserved on the equipment. 

Real Time PCR

The Genomics Core owns a QuantStudio 3 (Applied Biosystems) 96-well format RT-PCR instrument. The system support RT-PCR experiments using Taqman type probes, as well as SYBR green designed assays. The investigators can either bring their own reagents or can acquire the reagents through the Genomics Core. For pricing information, please contact us.

To reserve time on the instrument, please sign up using the calendar in our iLab system. Charges are on a per-hour basis. Cancellations should be performed 24 hours prior to usage. Otherwise, the user will be charged for the number of hours reserved on the equipment. 

Specific Taqman assays provided by IDT 

Sample Submission

We encourage all investigators to briefly discuss their experiment prior to submission of samples. RNA or DNA samples are directly submitted to the Genomics Core. The quality/quantity of the received nucleic acids will be evaluated using Bioanalyzer or TapeStation and Qubit. The Genomics Core staff will prepare libraries for Next Generation Sequencing depending on the preferred platform indicated by the investigator and perform the sequencing.

Please complete the online form and submit it to the Genomics Core. Samples will not be accepted without prior submission of the form.

Sample submission forms can be found under Genomics Core tab after signing in to our iLab system.

Pricing

Pricing varies depending on the services and whether the requester is from an internal or external organization. Contact us for quotes or log in to our iLab system.


The Genomics Core staff recommend briefly discussing your experiment prior to submission of your samples.

FAQs

Does the core provide RNA or DNA extraction services?

No, individual investigators are responsible for extracting nucleic acids.

What are the sample quality guidelines?

In order to ensure the most accurate results all samples should be checked for concentration, A260/280 as well as gel electrophoresis prior to submission.

Does the Genomics Core run quality assurance checks on submitted samples?

Yes. The Genomics Core staff will check all submitted samples by running samples on Agilent 2100 Bioanalyzer or 4200 TapeStation. If any sample fails QC at this point, the investigator will be notified. The investigator will then have the option to continue with the experiment or submit new samples. The core cannot make any guarantees for the quality of data that is generated using samples that do not pass initial QC checkpoints.

How are samples submitted?

All samples should be in either nuclease-free water or low-EDTA TE buffer. It is the responsibility of the researcher to provide samples in a buffer that is compatible with a library preparation. The form (linked to in the “Sample Submission” tab) should be submitted to the core. As a reminder, the Genomics Core will not accept samples without prior submission of the form. The Principal Investigator signature agreeing to pay the cost of the experiment and account number information for billing should be included with the form.   

How long until I get my results?

Typical turnaround time is around three weeks from time of receipt of samples and sample submission form. However, this will depend on the total number of samples provided by the investigator and other samples ready to be run. The Genomics Core will try to run a particular fixed number of samples per sequencing platform to reduce costs for each investigator. Investigators will be notified once the quality of their samples is assessed for a more accurate timing. 

Do I need to pay for the whole flow cell when I only have a few samples to sequence?

No. If your requested sequencing setup is one of our more popular options (e.g. 2x50bp) we can sequence your samples with other projects. We only charge for the requested number of reads, plus a buffer of a maximum of 10% extra. So, if you requested 100M reads and received 150M, you would only pay for 110M. If you received fewer reads than requested you would pay only for the received reads. 

Can I prepare my own libraries and just use a sequencer?

Yes, we can load user-prepared libraries on one of our sequencers. Depending on the requirements of the sequencing (single- or paired end, length, number of reads) we may be able to accommodate loading user-prepared libraries together with other libraries and only charge for a part of the run. However, this in not guaranteed and it requires coordination regarding the indices used for multiplexing to ensure compatibility of all the samples. We also require the use of UDIs. 

Do you perform data analysis?

The Bioinformatics Core will perform analysis, if requested. Please contact Bioinformatics Core staff for more details.

How long do you store submitted samples?

Samples will be kept until the experiment is completed. If the investigator does not indicate that further data will be required using the same samples, the remainder of the samples will be discarded (or returned to the investigator, if requested).

How long do you store experimental data?

Experimental data will be accessible to the investigator for one month. The investigator is responsible for downloading the data into their own servers.

Raw data will be archived by the Bioinformatics Core and stored for a minimum of one year. Requesting any data from the archive will incur an additional fee (contact the Bioinformatics Core for more details).

The investigator is responsible for downloading and storing the raw data into their own server for long term storage.

Do you accept projects from outside institutions?

Yes, the Genomics Core will provide services for institutions other than The Wertheim UF Scripps Institute. For specific projects or questions, please contact Genomics Core staff.


Contacts