Frequently Asked Questions

   

Questions we have been asked frequently cover the application process, as well as technical issues such as SNP typing. The final section discusses various other questions.

   

The application process

Q: Do I have to be NERC-supported to be able to apply to NBAF?

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.

Q: I have obtained a NERC grant – why do I have to complete a new application 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. We keep the work involved to a minimum (750 words). NBAF typically does a lot more than just running the sequences, so there needs to be a clear understanding of who does what, and the form helps us to sort this out. Overall the process has proved to be beneficial, with many projects being much refined or else improved to take advantage of new developments. While your application 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 application, even if we had it.

Q: Who should complete the application form?

The application form (and appendix!) should be formally submitted by the Principal Investigator. This is normally the Supervisor when a PhD student is involved, however the draft can be prepared by the visitor / PhD student provided the final version has been approved of and is submitted by the Principal Investigator.

Details of how to apply to the Facility

Q: When do I need to contact the Sheffield node by?

You will need to have sent the Sheffield node manager a draft of your application at least one month before the submission deadline, i.e., by the last Friday of February, April, June, August, October and mid December; this way, we can provide you with feedback ahead of the deadline.

Q: I am not sure how to fill in the form, can I get help?

The Sheffield Facility Manager Dr Deborah Dawson can provide advice and assistance when completing the form (and appendix). We can also advise on the feasibility of any proposed project and suggest improvements to hopefully clarify and add the full details required.

email : D.A.Dawson@Sheffield.ac.uk

Q: My project involves a postgraduate student, where do I enter his/her details?

If you plan for your student to visit the Facility, please enter his / her contact details under the "proposed visitor" section (7b), as well as their funding details under section (7c); if your student will not be visiting, but will benefit from the project, please do include their details under section (7c), as this information is relevant to NERC for annual reporting.

Q: I have submitted my application on schedule – when will I hear about the outcome of my application?

The Steering Committee makes decisions 6 times a year. You will then receive a NERC official correspondence one month later, i.e. 2 months following the application deadline.For more information and decision dates, consult the following webpage:

Decision dates

Q: How will I know if my application is accepted?

NERC will inform the Principal Investigator directly by email.

    

SNP typing

Q: 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 Edinburgh, Liverpool nodes and Sheffield nodes? 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 NBAF assistance via the NBAF-Edinburgh 454 sequencing node (or in some case via NBAF-Liverpool).

-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 NBAF 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 2 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.

Q: 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.

Q: Where can I get more information about SNP typing?

Please see our Technical Expertise webpage (or email Sheffield Facility Manager Dr Deborah Dawson).

Technical Expertise webpage

    

Various

Q: 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 also be tailored to the specific needs of each visitor.

Q: 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 the following webpage:

Requirements