Presentation

Presentation

The Genomics Core Facility is an IRCAN Facility dedicated to gene expression analysis. It provides knowledge and access to cutting-edge, medium-to-high throughput tools and technologies. It is open to all members of IRCAN, as well as to external academic or non-academic members of the scientific community.

It is located at the 5th floor of the Pasteur tower.

Managers

Managers

	Dr Gaël Cristofari Principal Investigator Head of the Genomics Core Facility Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
	Dr Christian Baudoin Staff Engineer Technical Manager of the Genomics Core Facility Tel: +33 (0)4 93 37 70 56 Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
	Nadine Fedou Administration & Billing Tel: +33 (0)4 93 37 76 98 Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Board

The executive board :

1. decides the strategy of the Core Facility (technologies, investment, pricing) ;
2. represents the users of the Core Facility.

The executive board meets twice a year. Its current members are :

Equipments

Equipments

qPCR		Biomolecule quantification
	2x Applied StepOne Plus (Life Technologies) Fast 96-well block		NanoDrop 2000 (Thermo Scientific) UV-Vis Spectrophotometer for microvolumes
	Applied 7500 (Life Technologies) Classical 96-well block		Bioanalyzer 2100 (Agilent) RNA, DNA and protein quantification and analysis by capillary electrophoresis
	Applied 7900HT (Life Technologies) Fast 96-well block TLDA 384-well block		Qubit 2.0 (Life Technologies) Fluorometer for specific DNA, RNA or protein dosage
Imaging systems		Plate readers
	Odyssey Classic (LI-COR) Infrared fluorescence scanner (quantitative western-blots, non-radioactive northern- & southern-blotting)		Centro XS LB960 (Berthold) Luminescence
	Typhoon FLA9000 (GE Healthcare - ex-Fuji) PhosphorImager, Fluorescence Scanner		TriStar LB 941 (Berthold) Absorbance, Fluorescence, Luminescence, BRET and BRET², FRET
Chromatin-IP (ChIP)		Next-Generation Sequencing
	Bioruptor Plus (Diagenode) Sonicator for microvolumes (6- to 12-samples in parallel)		Ion OneTouch System (Life Technologies) Emulsion PCR and bead (ISP) purification for Ion Torrent Sequencing
	SX-8G IP-Star Compact (Diagenode) Automated chromatine-IP (ChIP)		Ion Torrent PGM (Life Technologies) Next-Generation Sequencing Compatible with 314, 316 and 318 Chips
	Pippin prep (Sage Science) Preparative electrophoresis of nucleic acids with automated size selection (deep-sequencing library preparation)
Bioassays
	Luminex 100/200 (Luminex Corp.) Multiplex bioassays in microvolumes (up to 40 analytes measured in a single assay, including peptides, cytokines, nucleic acids, enzymes, ...) in a single well.
	Vitros 350 (Ortho Clinical Diagnostics) Measure of metabolites, ions, hormones and potentiometry in biological samples.

Booking

Access & Booking

With the exception of next-generation sequencing, Genomics Core Facility equipment is open-access after signature of the charter and online mandatory reservation. A small fee to cover the operating costs is charged by IRCAN to research teams based on their use.

For deep-sequencing, which is in its starting phase, projects are treated on a collaborative basis.

1. Send a brief description (few lines max) of the experiments and number of samples to:  This e-mail address is being protected from spambots. You need JavaScript enabled to view it
2. We will define with the demanding team: the feasibility, the costs, the degree of contribution of the Core Facility, the needs in bioinformatics for analyzing the results.
3. Library preparations, emulsion PCRs and deep-sequencing are performed by Christian Baudoin.
4. Bioinformatics is performed by the team of Gael Cristofari or by the demanding team.

qPCR Cost

qPCR Cost

Fees (excl tax) for qPCR use

Consumables (plastics and kits) are not provided by the Core Facility and need to be directly purchased by users.

The fees below are related to the use of the qPCR machines (contribution to the maintenance contracts) and are billed to the teams based on their use.

Recommended reservation time

Deep-sequencing Cost

Deep-sequencing Costs

Deep-sequencing on the Ion Torrent PGM (Life Technologies) is a 3-step process:

1. Library preparation from the biological sample (DNA or RNA)
2. Emulsion PCR (ePCR) and bead (ISP) purification
3. Semi-conductor deep sequencing on a Chip

Steps 2 & 3 are performed by Christian Baudoin except if an exceptional agreement was made with the Head of the Facility. Library preparation can be performed either by the demanding team or by the Core Facility after agreement on the protocol.

Some reagents, notably for step 1, might be purchased by the demanding team. Consumables (kits and plastics) for steps 2 and 3, and reagents for quality controls of the 3 steps are purchased by the Core Facility and billed to the demanding team as a percentage of their use.

Do not hesitate to contact us at: This e-mail address is being protected from spambots. You need JavaScript enabled to view it for precise pricing.

Examples of costs (complete costs excl tax for an IRCAN team) :

1. Somatic deep-sequencing of 46 oncogenes & tumor suppressor genes (Ampliseq Cancer Panel kit) from 10 ng of tumor genomic DNA (frozen or FFPE samples): 412 € (excl tax)/sample (for 4 samples).
2. Somatic deep-sequencing of 400 oncogenes & tumor suppressor genes (Ampliseq Comprehensive Cancer Panel kit) from 40 ng of tumor genomic DNA (frozen or FFPE samples): 1450 € (excl tax)/sample (for 4 samples).

Charter

Charter

To access to the Genomics Core Facility, users have to sign up the Charter. It can be downloaded here and the signed original should be given to Christian Baudoin.

Access to the equipment

The Genomics Core Facility equipment is open access to IRCAN members. Depending on the machines used, a reservation might be required and a fee can apply. Access to non-IRCAN members is possible upon agreement from the Head of the Core Genomics Facility if the equipment and personel is available.

Reservation

For the equipment below, reservation is mandatory and is done exclusively online on the IRCAN website. A confidential user ID and password is given to the principal investigator of each research group. These codes allow access to the reservation portal and to the follow up of reservations.

Equipment with MANDATORY online reservation :

- qPCR 7900 HT
- qPCR 7500
- qPCR StepOne Plus 1
- qPCR StepOne Plus 2

Equipment without reservation :

- Luminometer CentroXS
- Plate reader Tristar
- Bioanalyzer 2100 Agilent
- Pippin prep
- IP-Star
- Bioruptor UCD-300
- Typhoon FLA9000
- Odyssey Licor
- Nanodrop 2000

Responsibilities and Commitments

1. Users commit themselves to follow user's and cleaning protocol of the equipment.
2. Only Applied Biosystems plastics are allowed on the qPCR machines. For any other plastics, ask the technical manager.
3. It is strictly forbidden to install softwares on the Genomics Core Facility computers.
4. Recommended reservation times for qPCRs: 1 hour for the 7900HT and StepOnePlus qPCRs, 2 hours for the 7500.
5. User data should be saved in the « Experiments » folder on the hard disk of the qPCR computers. This storage is temporary (a few days).
6. The users have to transfer and save their data files to their own storage systems in a regular manner. Data stored on the qPCR computers will be erased without notice during regular maintenance processes to avoid hard disk overloading.
7. The working space and equipment should be cleaned after each use.
8. Any personal material, reagent, sample, garbage should be removed after use. Non-identified reagent/sample/garbage will be trashed.
9. Equipment should not be used for unusual applications without prior agreement of the technical manager of the facility.
10. Mis-use of equipment, which would lead to equipment damage, will be charged to the research group involved.
11. Any dysfunction or technical incident should be immediately reported by email to the technical manager This e-mail address is being protected from spambots. You need JavaScript enabled to view it .

Acknowledgements and publications

The Genomics Core Facility will be NECESSARILY cited in the acknowledgement section of any publication for which an equipment of the facility was used. Please use the following sentence: "We thank the IRCAN Genomics Core Facility for providing access to [qPCR for example]". A copy of the articles will be given to the technical manager after publication. If the levels of contribution in the work is significant (particularly for deep-sequencing), the facility members will be included as co-authors in publications. Intellectual property rules from INSERM will apply.

Address

Address

IRCAN - Genomics Core Facility Medical School - 5th Floor 28 Av de Valombrose 06107 NICE Cedex 02 FRANCE                   Tel : +33 (0)4 93 37 70 56