FAQ

 

1. How can I work with Edinburgh Genomics?

We are an open-access academic facility, and are happy to work with researchers on a "fee for service" basis, or as a full collaborator. We are happy to provide just a quote for a piece of work where you know exactly what you want, or help you develop an idea and do the work in full collaboration. We pride ourselves on being able to engage with the entire research process, from project design, grant writing, project execution, data analysis and results write up (posters, papers, presentations etc).  Please get in touch through our contacts page and a member of our project team will contact you.

Please do contact us early in your experimental planning or grant writing process so that we can best help you write a successful application.

2. What sort of technologies does Edinburgh Genomics have? What can Edinburgh Genomics do?

We provide a complete genomics service, from sample QC, through library production, sequencing/data collection, and data cleaning to in-depth analysis. We offer all modes of data generation - DNA sequencing (in all its many forms), RNA sequencing (in all its many forms), Sanger sequencing, microarrays and SNP chips. We deliver data from a single Sanger read through to multi-whole genome resequencing projects involving tens of Terabytes of data. Similarly our Bioinformatics support ranges from data QC through to management of major genome sequencing and analysis projects, and includes advanced training.

Edinburgh Genomics currently has four main areas of expertise. We do:

Illumina sequencing on HiSeq X, 4000 and 2500 and MiSeq instruments. Whether you want to sequence a bacterial genome, or the genome of a mammal, survey a microbiome to identify the species and genes present, count mRNAs, ncRNAs, smallRNAs, or other molecules, identify and score genetic variants, or explore the epigenome of your study system, Illumina sequencing, with read lengths from 50 to 300 bases, and an output of 6 Gb to 55 Gb per lane, is our "workhorse" technology. Contact us. 

Sanger sequencing on AB3730 instruments. This service is available to all University of Edinburgh researchers, and others on application. Contact us.

Array-based counting of transcripts or copy number variation using stock or custom microarrays, and Variant detection using SNP chips. Contact us.

Bioinformatic analyses ranging from exacting data QC through to in-depth exploration of the genome biology of complex systems. We also offer Advanced training in bioinformatics, including bespoke training for research groups (see here for the current schedule of workshops). Contact us.

3. How do I get a quote from Edinburgh Genomics for a project I want to do?

Please fill in the enquiry form on our "Contact" page. Remember to tell us what your deadlines are, and please do give us as much information as you can about your needs. A member of our project team will contact you as soon possible to discuss the project in more depth and will develop a quotation to deliver to your project specifications. Please allow a week to 10 days for this process.

4. How much DNA or RNA do I have to supply? How should I ship it?

Please see our Sample requirements page for information on sample preparation, sample QC and the amounts we need for different library preparation methods. If you have any questions, please contact the member of the project team you have been discussing your project with directly.

5. How much will it cost?

Edinburgh Genomics is a "cost recovery" facility: we must recover from the services we offer the full cost of delivering them. It is very hard to give simple guidelines for how much a sequencing experiment will cost. Suffice to say that Edinburgh Genomics prides itself for being not only high-throughput and high-quality, but also competitive on price. When you discuss your needs with our project team, we will indicate what our prices will be. Our large throughput means we can negotiate good deals from suppliers, especially if the reagents are all for one project. As we are a full cost recovery facility, it is hard for us to offer discount where the size of the project does not attract additional interest from suppliers.

We are required to charge VAT at a non-zero rate for projects with collaborators/customers outside the University of Edinburgh unless a formal collaboration agreement is in place. Do contact us to discuss this.

 

6. How do I get my data back from Edinburgh Genomics? How long do you store data for?

 

We use a secure system called Aspera to deliver data back to collaborators. Aspera is very fast (much faster than ftp for example) and is very secure. When your project data are ready for download, you will be contacted with a login name and password, and given a link to your data. Noone else can see your data. If it is the first time you have used Aspera, you will need to download a very small client application. If you have any problems with Asopera, do contact our project team.

We leave next generation sequencing data on our live website for one month after we have notified you, and guarantee to store the data securely on local discs for three months after notifying you it is ready. You can ask us to keep it for longer (at cost).

 

7. How long will it take?

 

Again it is hard to give exact timings for every project in a general response to this question, but we aim to turn round samples as fast as we can, and to deliver analyses back to collaborators within an agreed timeline. When we set up a project with you we will give you an estimate of how long we expect it to take.

For Sanger sequencing, we turn samples around in 2 working days.

For user supplied next generation libraries and small data volumes, turnaround can be very fast (from 3 days). For larger projects involving hundreds of samples and terabases of data, obviously, turnaround is longer.

 

8. I want to do a project through the NERC Biomolecular Analysis Facility: how should I contact you?

 

For NERC NBAF projects, please use the contact form as for other enquiries. In the case of research grant funding rounds and the Pilot Projects Competition, NBAF has set deadlines for researchers contacting the facility in advance of the grant application submission deadlines. Please do contact us early in your grant writing process so that we can best help you write a successful application.

 

9. What happened to ARK-Genomics and The GenePool?

 

ARK-Genomics and The GenePool merged to form Edinburgh Genomics in August 2013. We are still an academic genomics facility and we will continue to work with you, collaborate, and provide access to state-of-the-art genomics technologies and bioinformatics. If you were a collaborator or customer of ARK-Genomics or The GenePool, we hope that the major difference in the way that we work with you will be that we offer more, better and faster service.