Genomics Core

Jupiter, Florida Campus

Welcome to the Genomics Core at Scripps Research, Florida!

Our goal is to provide investigators in our Jupiter, Florida campus as well 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 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:

  • Ion Proton (Ion Torrent)
  • NextSeq 500 (Illumina)
  • MiSeq (Illumina)


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 transcriptome sequencing (polyA enrichment or rRNA-depletion)
  • Small RNA sequencing
  • Ribosome profiling
  • Ultra-low input RNA sequencing
  • Single cell transcriptome profiling (using 10X chromium system)
  • Regulatory DNA or RNA interactions with proteins (RIP-seq, ChIP-seq) analysis
  • Splice variant quantification

For more information, please contact:

  Pabalu Karunadharma, Ph.D.
  B206/B244b
  Ph: (561) 228-2493
  pkarunad@scripps.edu


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]

Online Submission for Sample QC (Bioanalyzer/Tapestation) [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.

Please use our online booking system to reserve a machine. 

If you will not use your reserved time, please cancel your time 24 hours in advance to prevent charges. 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 $185 $199
Sequencing 200 bp reads (80-100 M total reads) using Ion Chef templation+ $1,415 $2,618 $2,816
*price per run if doing two sequencing runs.  For single run $1,615.00
MiSeq
Sequencing 2x50bp (15M paired-reads) $1,110 $2,054 $2,209
Sequencing 2x75bp (25M paired-reads) $1,210 $2,239 $2,408
Sequencing 2x150bp (15M paired-reads) $1,355 $2,507 $2,696
Sequencing 2x250bp (15M paired-reads) $1,490 $2,757 $2,965
Sequencing 2x300bp (25M paired-reads) $1,870 $3,460 $3,721
Millions of reads
NextSeq 500
Sequencing 2x40bp (400M paired-reads) $1,815 $3,358 $3,612
Sequencing 2x75bp (400M paired-reads) $3,310 $6,124 $6,587
Sequencing 2x75bp (130M paired-reads) Mid-output $1,400 $2,590 $2,786
Sequencing 2x150bp (130M paired-reads) Mid-output $2,090 $3,867 $4,159
Millions of reads
Library preparation for Illumina sequencing (library prep cost only)
Single-cell/ ultra low input mRNA-seq (Clontech SMART kit) $265 $490 $527
Ultra low input total RNA-seq (Clontech stranded total RNA pico) $275 $509 $547
Total RNA-seq library prep (NEBNext Ultra II directional) $251 $463 $498
mRNA-seq library prep (NEBNext Ultra II directional) $215 $398 $428
Small RNA-seq library prep (BioO NextFlex kit v3) $230 $426 $458
Nugen Ovation SoLo total RNA-seq (10pg-10ng) + AnyDeplete option $275 $509 $547
ChIP-seq library prep 500pg-1ug (NEBNext DNA Ultra II)  $180 $333 $358
Ribosome footprinting (includes PNK treatment+ library prep) $255 $472 $507
Bioinformatics for standard projects - per sample cost $100 $185 $199
25 million paired-end 2x40bp reads for RNA-seq, ChIP-seq $125 $231 $249
Other Services
Gel size selection and purification $60 $111 $119
Dnase I treatment $30 $56 $60
Qubit
Per sample $5 $9 $10
Agilent Bioanalyzer 2100 + Qubit quantification
Agilent RNA Nano kit $125 $231 $249
Agilent RNA Pico $125 $231 $249
Agilent HS DNA $150 $278 $299
Agilent DNA 1000 $125 $231 $249
Agilent Small RNA kit $135 $250 $269
Price are per run. Each run can hold 11-12 samples.
Agilent TapeStation 2200§
HS DNA (10-100pg/ul) $7 $13 $14
DNA 1000 (10-50ng/ul) $6 $11 $12
§Price per 2 samples. Each Tape can run samples in duplicate up to 16.
Real Time PCR Machines
qPCR quantification of NGS library $30 $56 $60
Charge per hour for use of instrument $19 $35 $38
Sonicators (Covaris & Bioruptor)
Charge per hour $25 $48 $50
Covaris tube $6 $11 $12

 

 

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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