Genomics Core

Jupiter, Florida Campus

Welcome to the Genomics Core at Scripps Research, Florida!

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

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 owns the latest 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. Research can also be performed on a collaborative basis with the Genomics Core staff for protocol optimization to meet each investigator’s demands. 

The Genomics Core maintains and operates the following platforms: 

  • SOLID5500XL (Life Technologies)
  • Ion Proton and Ion Personal Genome Machine (PGM) (Ion Torrent)
  • NextSeq 500 (Illumina) 
  • MiSeq (Illumina)
  • Affymetrix GeneChip

 
We also provide the following equipment: 

  • Ion Chef system (Ion template preparation, chip loading, and Ampli-seq library prep for Ion Torrent platforms)
  • Sonicators (Bioruptor and S2 Covaris)
  • Real time PCR machine (Step One Plus)
  •  Agilent 2100 Bioanalyzer
  • Agilent 2200 TapeStation.

 
These technologies allow the core to support a wide array of experimental approaches including: 

  • Whole gene expression profiling
  • whole transcriptome sequencing (polyA enrichment or rRNA-depletion)
  • small RNA sequencing
  • Ultra-low input and single-cell RNA sequencing
  • Regulatory DNA or RNA interactions with proteins (RIP-seq, ChIP-seq) analysis
  • Splice variant quantification
  • Copy number variation
  • Secondary validation of array data
  • Whole genome association studies

 
All work performed by Scripps Research Florida Genomics Core Facility that supported your research must 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 Scripps Research Florida Genomics Core.

Please see the ABRF guidelines for authorship for personnel working in core facilities: https://abrf.org/authorship-guidelines

 

Services

Core Services and Approval Invoice [PDF] 

Online Form [HTML]

Please complete the online form and submit it to the Genomics Core. Then fill out the "Core Services and Approval Invoice", and bring it signed by the Principal Investigator financing the services, together with the samples. Samples will not be accepted without prior submission of both forms.

Guidance document [Word docx. For downloading]:

Please use our online reservation system to reserve a machine. For a quick reference guide on how to log in and reserve a machine, please click here. If you are not a Scripps Research employee, please contact the Genomics Core staff for a reservation.

Training on every single machine is required for first-time users. Please coordinate with the Genomics Core staff for training.

The two real time PCR machines are charged based on a per hour basis. Please consider this when reserving time on these machines. If for some reason you will not use your reserved time, please cancel your reservation 24 hours in advance to prevent charges. Investigators will be charged for the whole booked time if the reservation is not cancelled 24 hours in advance. For pricing information, please click here.

For booking your time on Step One Plus (Applied Biosystems) real time PCR, click here.

  • For booking your time on S2 Covaris sonicator, click here.
  • For booking your time on Bioruptor sonicator, click here.
  • For booking your time on Agilent 2100 Bioanalyzer, click here.

To request a quote, please contact the Genomics Core Director, Pabalu Karunadharma. The following table provides only with estimated (not final) prices for the services provided by the Genomics Core.

SCRIPPS FLORIDA GENOMICS CORE RATES
External Rates
Description Internal Rates Non-Profit/Universities Profit Organizations
Next Generation Sequencing & Microarray
Ion Proton**
Amplicon library preparation (price per sample) $100 $190 $199
Sequencing 200 bp reads (80-100 M reads) using Ion Chef templation† $1,500 $2,850 $2,985
†price per run if doing two sequencing runs.  For single run $1,700.00
MiSeq
Sequencing 2x75bp (25M* paired-reads) $1,1130 $2,147 $2,249
Sequencing 2x150bp (15M* paired-reads) $1,280 $2,432 $2,547
Sequencing 2x250bp (15M* paired-reads) $1,410 $2,679 $2,806
Sequencing 2x300bp (25M* paired-reads) $1,780 $3,382 $3,542
NextSeq 500
Sequencing 2x40bp (400M* paired-reads) $1,725 $3,278 $3,433
Sequencing 2x75bp (400M* paired-reads) $3,120 $5,928 $6,209
Sequencing 2x150bp (400M* paired-reads) $4,880 $9,272 $9,711
*Millions of reads
Library preparation for Illumina sequencing (library prep cost only)
Single-cell/ ultra low input mRNA-seq (Clontech SMART kit) $265 $504 $527
Ultra low input total RNA-seq (Clontech stranded total RNA pico) $275 $523 $547
Total RNA-seq library prep (NEBNext Ultra II directional) $251 $476 $498
mRNA-seq library prep (NEBNext Ultra II directional) $215 $409 $428
Total RNA-seq library prep (Illumina TruSeq) $285 $542 $567
mRNA-seq library prep (Illumina TruSeq) $225 $428 $448
Small RNA-seq library prep (BioO NextFlex kit v3) $230 $437 $458
Nugen Ovation SoLo total RNA-seq (10pg-10ng) + AnyDeplete option $275 $523 $547
ChIP-seq library prep 500pg-1ug (NEBNext DNA Ultra II)  $200 $380 $398
ChIP-seq library prep 10pg-10ng (Clontech DNA SMART ChIP-seq kit) $225 $428 $448
Ribosome footprinting (includes PNK treatment+ library prep) $255 $485 $507
Amplicon library prep (PCR reaction purification + adding adapters) $250 $475 $498
Bioinformatics for standard projects - per sample cost $100 $190 $199
25 million paired-end 2x40bp reads for RNA-seq, ChIP-seq $108 $205 $215
Other Services
Gel size selection and purification $60 $114 $119
DNase I treatment $30 $57 $60
Agilent Bioanalyzer 2100***
Agilent RNA Nano kit $43 $82 $86
Agilent RNA Pico $47 $89 $94
Agilent HS DNA $70 $133 $139
Agilent DNA 1000 $45 $86 $90
Agilent Small RNA kit $60 $114 $119
Agilent TapeStation 2200+
HS DNA $9 $17 $18
HS RNA $8 $15 $16
+ Price per sample. 
Qubit
Per sample $5 $10 $10
Real Time PCR Machines
Charge per hour for use of instrument $19 $36 $38
Sonicators (Covaris & Bioruptor)
Charge per hour $25 $48 $50
Corvaris tube $6 $11 $12

*Possibility of multiplexing up to 18 samples per run.

**Possibility of multiplexing up to 96 samples per run.

***Prices are per run. Each run can hold 10 or 11 samples each.

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. 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 library preparation. Two forms (linked to in the "Forms" tab) should be submitted to the core. As a reminder, the Genomics Core will not accept samples without prior submission of both forms. The Principal Investigator signature agreeing to pay the cost of the experiment and account number information for billing should be included in one of the forms.   


How long until I get my results?

Typical turnaround time is around two 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 you perform data analysis?

The Bioinformatics core will perform preliminary data analysis. If further analysis is required, please contact Bioinformatics Core staff. 


How long do you store submitted samples?

Samples will be kept until the experiment is completed, and the investigator confirms that no further data is required using the same samples. At this point, the remainder of the samples will be returned to the investigator.


How long do you store experimental data?

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

Raw data will be stored by the Genomics Core share, and stored for a year. The investigator is responsible for downloading the raw data into their own server once this time expiries. Notifications will be sent once month priori to the deletion of either raw or analyzed data.


What are the costs for each experiment?

For pricing, please check out the Genomics Core ratesFor large scale projects or specific discounts, contact Genomics Core staff.  


Do you accept projects from outside institutions?

Yes, the Genomics Core will provide services for institutions other than Scripps Research Florida. For specific projects or questions, please contact Genomics Core staff.

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