Frequently Asked Questions

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Can NEOF support my research? Who can access NEOF?

NEOF is pleased to support the academic community via 4 different access routes:

I am applying for a NERC grant. How do I get support from NEOF?

Where NEOF has been approached to discuss project feasibility and provide quotes prior to a NERC grant application, we will issue quotes on the basis that this work is done in collaboration with NEOF, that the NEOF quotes issued will be added to the facility costs on the JeS form, and that a NEOF access form will be completed after the award has been made, but before any work can be submitted to NEOF.

I have a NERC grant but I didn’t include NEOF in my application. How can I get support?

For NERC-funded grants in which NEOF quotes were not included as facility costs on the JeS form (and therefore the funds allocated for this work are not held by NEOF), a NEOF Access Form can be completed to run associated projects in collaboration with NEOF at the preferential NEOF rates. If a NEOF Access Form is not completed for such projects, applicants can instead request support directly from the University of Sheffield Molecular Ecology Lab and/or the University of Liverpool Centre for Genomic Research; higher rates may then apply. The PI will be invoiced for this work.

I am a PhD student or supervisor. How do we get support from NEOF?

For studentships within the NERC remit, access to the NEOF Visitor Facility can be requested via completion of a NEOF Access Form, which is subject to approval by NEOF’s independent steering committee. If appropriate, applications can include sequencing costs up to an indicative value of £10,000; projects are run in collaboration with NEOF. The Access Form should be completed by or with the supervisor (listed as the PI) following discussion with NEOF staff on experimental design, sample numbers, work plan, etc – which must be initiated via our Enquiry Form. Applications are scored for the quality of the science and hypothesis-driven research is encouraged. If your application is approved, you would attend the NEOF Visitor Facility at Sheffield for an agreed period (maximum 6 months), to carry out lab work and analyses under the supervision of our staff. We can provide bespoke training and support regarding the data analyses if required.

Is there any other route to get support for work done at NEOF?

NEOF supports Pilot Projects via the annual Early Career Researcher Genomics pilot competition and the Multi-omics Independent Researchers pilot competition (for Genomics, Metabolomics and Proteomics projects). A maximum of 5 days’ access to the NEOF Visitor Facility at Sheffield can be added to an application to the Genomics pilot competition, if required (to complete DNA extractions, for example).

I am applying to UKRI but not NERC. How can I access support from NEOF?

For grant-supported work falling both within and outside of the NERC remit, or not supported by UKRI, please enquire to see if our laboratories can help.

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

Is my work within NERC remit?

The research areas supported by NERC are included in UKRI’s remit page.

How do I know that my institute is eligible to apply for access to NEOF?
Is there a limit on the size of project that NEOF can support?

No, but if a project is expected to cost more than £100,000 we will discuss the funding arrangements with you during the initial enquiry stage.

I have obtained a grant from NERC – why do I have to complete an access form?

In practice, many grant applications do not include much technical detail and we do not get very involved at that stage. We do not routinely see or comment on the full application and, even if we did, investigators often change their plans. NERC Facilities are therefore required 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 NEOF access form helps us to sort this out. Overall, the process has proven 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 that you will be asked to further refine your plan. The other requested 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.

I am applying for a grant from NERC. Am I obliged to plan to get my analyses done by NEOF?

No, but NERC requires that you obtain an equivalent quality of service and price from the alternative provider. Alternative providers, which are often based overseas, may offer lower headline prices but there is usually no equivalent support for experimental design or data interpretation, and there may be conditions regarding data ownership. NERC requires value for money rather than the lowest possible price, as the latter can be a false economy.

I have obtained a grant or studentship from a source other than NERC. Can I apply for access to NEOF?

You do not need to be NERC-supported to access support from NEOF; providing the focus of your proposed research project is within the remit of NERC, you can submit an application irrespective of which organisation supports your research.

When will I hear the outcome of my request for access to NEOF?

If your project is funded by a NERC grant, it will be fast-tracked and you should receive the decision within one month of your request.
For applications to the pilot project rounds, due to the volume of applications, you should typically hear the decision after three months of the deadline.
For all other projects, you should receive the decision after approximately two months, although at busy times it may be slightly longer.

How will I know if my application is accepted?

NERC will inform the Principal Investigator directly by email.

Who should complete the NEOF access form?

The NEOF access form should be formally submitted by the Principal Investigator. This is normally one of the supervisors of the project, but applications can be drafted by any member of the team, including a PhD student, provided the final version is approved and submitted by the Principal Investigator or Co-Investigator.

Are there any deadlines for submitting a form to request access to the NEOF (including Visitor Facility)?

Outside of the pilot rounds, there are no deadlines to request access and forms can be submitted all year round.

Please note that the reviewing process takes two months after which you will hear if your work is approved for support, so you should factor this time when planning sampling and proposing timings of lab work.

I would like to speak to someone about accessing the NEOF Visitor Facility at Sheffield, can I get help?

Please send an enquiry to NEOF where a member of the team will 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.

My project supports a postgraduate student; what is the level of support?

Successful applicants will be required to cover travel, accommodation and subsistence for the visitor but access to the NEOF-Visitor Facility will be free and provide 1 to 1 training and consumables, including DNA sequencing. Supported visitors will also be given priority to the free bioinformatics training courses.

Can I add my postgraduate student as a Co-Investigator?

Under NERC rules postgraduate students are not eligible to be named as Co-Investigators.

My project involves a postgraduate student, where do I enter their details?

If you plan for your student to spend time at the NEOF Visitor Facility in Sheffield then please enter his/her contact details in the ‘Proposed Visitor’ section, as well as their funding details where requested; if your student will not be visiting, but will benefit from the project, please still include their details, as this information is requested by NERC in our annual reporting.

Is there a NEOF pilot scheme for PhD students?

Postgraduate students cannot be Principal or Co-Investigators for any NEOF projects. But PIs can apply to the pilot competitions (ECR and Independent) to support work being done by their students. The main direct access route for student support is provided by the Visitor Facility, which unlike the pilot scheme, accepts applications year-round.

What is the difference between a standard application and the pilot competition?

The pilot competition targets small pilot/development sequencing projects to be undertaken at NEOF. These projects are aimed at the generation of preliminary data or proof of principle in advance of full research grant proposals, particularly when it is necessary to demonstrate the applicability or the technical feasibility of new techniques or approaches to NERC-relevant research problems. Finally, standard applications are reviewed as received, whereas the pilot competition is an annual competition.

Exactly what platforms and capabilities do you have available?

We give an outline of our platform on our capabilities page, but because of the rapid pace of omics the precise details change frequently and can be difficult to navigate for a non-specialist. Instead, we prefer users contact us through an enquiry form. This allows us to concentrate on the scientific question and finding an appropriate experimental design to answer it.

Can I get help with my population genetics data analysis?

NEOF has staff dedicated to helping users with the downstream analysis of the genetic datasets they generate, regardless of marker type.
Help can be obtained for a wide variety of genomics methods, including:• Species identification from sequence data (e.g. using DADA2)
• read alignment, variant calling and downstream population genetics analysis (e.g.  BWA, SAMtools, bcftools, VCFtools, ANGSD, etc)
• Population genetic structure (e.g. fastSTRUCTURE, STRUCTURE, PCA)
• Inference of population history and effective population sizes from genomic data (e.g. PSMC analyses)
• Detecting signatures of selection and selective sweeps with genomic data (e.g. REHH, BayPass)
• Parentage and mating system studies using appropriate packages (e.g. Sequoia, Colony)
• Molecular quantitative genetics and gene mapping (e.g. GWAS analyses, genomic prediction, estimating genomic relatedness with packages such as GCTA, Plink, R libraries etc)
The dataset must be generated in NEOF and support will be provided to attendees of the NEOF Visitor Facility, located in Sheffield.

Where can I find a price list of services?

Costs are updated very frequently and don’t scale linearly with number of samples. We also want to focus on delivering the best science possible through good experimental design. Please use our enquiry form to discuss your study and we will provide a quote.

What are the sample requirements for sequencing?
How do I get good quality DNA

We have produced this handy flowchart and staff at the visitor facility will be happy to discuss further Sample Storage Flow Chart_9jan2024

What are the requirements for the submission of first round PCR products for PCR2 tagging and sequencing?
How do I decide what read length is best for sequencing my amplicons using the MiSeq?

Please see https://emea.illumina.com/systems/sequencing-platforms/miseq/specifications.html

Product sizes between 150-250 bp require a 2x150bp MiSeq v2 run

Product sizes between 250-450 bp requires a 2x250bp MiSeq v2 run

Product sizes between 450-550 bp require a 2x300bp MiSeq v3 run

When selecting the best read length to use on MiSeq sequencing you should consider whether you need overlap between the forward and reverse reads (usually the case), and, if so, how much overlap. We typically aim for ~50 bp overlap, so anything up to 250 bp should be fine on a 2×150 bp run, anything up to 450 bp should be fine on a 2×250 bp run, and anything up to 550 bp on 2×300 bp. We can still sequence larger products, but stitching forward and reverse reads together will probably not be possible, so this will need to be taken into account during analysis. It’s also worth bearing in mind that for things like ITS amplicons, which have a wide range of product sizes from different species, if we use a stitched-read approach for analysis, this will exclude any species generating products >550 bp. The MiSeq is recommended for studies of species diversity from environmental DNA samples and used in diet analyses. If you have other types of projects in mind and want to discuss our other sequencing platforms, please get in touch!

FAQ for metabolomics projects
FAQ for proteomics projects