Frequently asked questions
Questions we have been asked frequently cover applying or access, facilities available, visit arrangements, techniques, sample requirement and data analyses.
Do I have to be NERC-supported to be able to apply to NEOF?
No, providing the focus of your proposed research project is within the remit of NERC, applications can be submitted by researchers supported by any source of funding.
I have obtained a NERC grant – why do I have to submit a NEOF access request form?
In practice, many grant applications do not include much technical detail and we do not get much involved at that stage. We don't routinely see or comment on the full application and, even if we did, investigators often change their plans. So, the view is that a facility needs to review the relevant aspects of a project.
NEOF typically does a lot more than just running the sequences, so there needs to be a clear understanding of who does what, and the access form helps us to sort this out. Overall discussion has proved to be beneficial, with many projects being much refined or else improved to take advantage of new developments.
While your application to access NEOF facilities will not be rejected, it is possible for you to be asked to further refine your plan. The other information is either basic contact information or information that we have to return to NERC annually about our users but that we could not necessarily extract from your full NERC grant application, even if we had it.
Who should complete the application form?
The NEOF access form should be formally submitted by or approved of the Principal Investigator. This is normally completed the Supervisor when a PhD student is involved.
See our page on how to apply.
Can my PhD student be a co-investigator?
If PhD students are due to visit the facility, they should be listed in the "Visitor" section on the access form.
I would like to chat to someone about accessing the NEOF Visitor Facility at Sheffield, can I get help?
The Visitor Facility Manager Dr Deborah Dawson can provide advice and assistance. We can also advise on the facilities and expertise available, information regarding visit arrangements, feasibility of any proposed project, clarify the techniques we support and any important project/sample details requiring consideration.
What is the set-up time a post-doc would have to do for SNP typing? How much of that could be done at the Liverpool and Sheffield? How much technical support is provided by Sheffield staff?
The SNP typing process is as follows:
- SNP mining: This is carried out by the user, either away from site from a published genome or with NEOF assistance via Liverpool (sequencing).
- DNA preparation and quantification: This is carried out by the user either at Sheffield or off-site.
- SNP design and Assay (Illumina provide a 'ready to go' kit).
- Assay run on the BeadExpress: This is carried out the user at Sheffield under the supervision of NEOF staff at Sheffield.
- SNP Data analysis (carried out by the user either at Sheffield or off-site)
Running the plates on the BeadExpress is very time consuming and the maximum rate is two plates run per person per week. This is also pretty full-on work with little downtime.
Since it is fairly technically demanding it would require a suitably experienced lab person to visit Sheffield who we would then train up to use the BeadExpress.
How vital is the concentration of DNA to be used for SNP typing?
SNP development sample requirements: At least 5 micrograms of (pooled) high-quality cDNA is required from which the SNPs would be initially identified by sequencing.
For the SNP genotyping of each individual, 250 ng of genomic DNA at a concentration of 50 ng/ul (quantified using spectrophometer/fluorometer). DNA should be buffered in 10 mM Tris-HCl pH 8.0, 1mM EDTA.
Individuals are genotyped in multiples of 480, so experiments should be designed with this in mind.
Where can I get more information about SNP typing?
Can I get help with my data analysis?
The Sheffield node has member of staff dedicated to helping users with the downstream analysis of a genetic dataset, independently of the type of genetic markers used.
Help can be obtained with a wide variety of population genetic methods, including basic tests of Hardy-Weinberg and linkage equilibria, calculating indices of genetic diversity, F-statistics and genetic distances between populations, as well as algorithms detecting the underlying genetic structure among a set of individuals, population divergence times and past demographic history.
We also provide support for relatedness and paternity studies. Help can, of course, be tailored to the specific needs of each visitor.
My application has been funded and includes development of a microsatellite library. What quality starting DNA do you need?
Details of what we require are listed on our Microsatellite Libraries webpage.
The NERC Environmental Omics Facility (NEOF)
Making state-of-the-art molecular genetics facilities and training available to the UK science community.