Terms and FAQs

Application support

Currently we are able to offer full support for genomic denovo/resequencing, ChIP-Seq and RNA-seq. This includes library preparation and downstream analysis.

Other applications (e.g. Meth-Seq) require the user to generate these libraries. Preparations for these types of runs are highly dependent on the experiment and as such they are best left to investigators.

RNA-seq spike-in

Note that we usually spike-in 1% synthetic controls listed on the sample preparation page. If any doubt, please contact us.

Run timings

Please note that this is highly dependent on the type of application, your desired read length and how many other samples we have from other users.

Some sequencers have relatively short run times of a few hours or days (e.g. Illumina MiSeq and PacBio). Other sequencers require a relatively large number of samples to run economically (e.g. Illumina Novaseq).

We cannot book a particular run date in advance. Samples are queued according to date of receipt. Samples are regarded as being in the queue when they are delivered – we cannot ‘book space’ for samples in advance.

On receipt of your sample, we will email the designated contact person to acknowledge receipt and to give a first estimate of when the sample will be processed (i.e. its place in the queue).

Sample delivery

Please ensure that you follow the preparation guidelines. We will not accept samples which do not meet these criteria or which do not arrive with the requested information.

Sample failure

Should any sample fail our quality criteria due to reagent or other sequencing failure we will inform you and run the sample again on the next sequencing run.

Sample storage

All samples will be kept for a period of 3 months after completion of a successful run. Any samples which need to be returned should be collected within this time. External users are responsible for organizing shipment of return samples.

Any samples not collected within this time-frame will be destroyed.

Frequently asked questions

If you have any queries that are not answered here, or would like to discuss your requirements further, please do not hesitate to contact us.

How do I know when my results are ready?

As soon as a run is completed and the pipeline analysis has finished, an email will be sent to you automatically to give you instructions on how to access your data. This is done via direct download from the University of Exeter cloud storage.

Are my results private?

Yes. You will be sent a secure download link.

How large will my results be?

This depends on how much sequencing you have requested. For an SP flowcell with 50 PE sequencing you can expect up to 60-80 Gb of data to be generated depending on the application, for the largest S4 flowcell 3000 Gb data may be generated. Please make sure you have space to store it and that you allow at least 12 hours for it to download depending on your connection.

How long will my results be available?

Your results will be kept online for at least 3 months and archived for at least 3 months. Nonetheless, please ensure you backup your data.

What format will my results be in?

This in large part depends on the type of experiment that is being run. However for any experiment, you will always receive the raw data prior to alignment (e.g. For Illumina sequencing, the FASTQ file containing the fragments which were sequenced). This is so that you can do your own analysis using alternative programs if necessary.

How long does the sample stay in the sequencer?

A Novaseq and MiSeq run takes roughly 2-4 days to run; the sequencer can deliver data in as little as 3-5 days.

How involved will I be in the library preparation?

We can prepare your libraries for the majority of sequencing projects. We will need you to provide high quality nucleic acid at the right concentration and with suitable QC information.

We are able to provide training for UoE PhD students in specific library preparations if requested.

For bespoke libraries such as HiC and ChIPseq where crosslinking or immunoprecipitation is required we can advise you, however you will need to prepare your own libraries, or pre-prepare the DNA so we will need to work very closely together. Please contact us to discover more.

Acknowledging the service

If you have used data produced by the University of Exeter Sequencing Service, you are obliged to acknowledge the facility and the appropriate grants that support us. Failure to do this could make us ineligible for future funding.

Acknowledgements (as instructed below) should be included in:

Papers (including preprints)
Conference Presentations
Posters

We also need to compile PDFs of these to report back to funding bodies on a yearly basis. Please also send a PDF copy to the sequencing service to assist us in compiling a yearly progress report.

Acknowledgement text to use

For any project using the PacBio or PromethIon Sequencers or MRC based ISCA nodes:

“This project utilised equipment funded by the UK Medical Research Council (MRC) Clinical Research Infrastructure Initiative (award number MR/M008924/1)”.

In addition, you should acknowledge the use of ISCA by adding an Unclassified Label “ARC – Isca” in Symplectic after you have submitted the paper. For more details see the Isca guide (pdf).

For any project using the Illumina NovaSeq 6000 or Chromium 10X:

“This project utilised equipment funded by the Wellcome Trust (Multi-User Equipment Grant award number 218247/Z/19/Z)”

For any project using the Illumina HiSeq or MiSeq:

“This project utilised equipment funded by the Wellcome Trust Institutional Strategic Support Fund (WT097835MF), Wellcome Trust Multi User Equipment Award (WT101650MA) and BBSRC LOLA award (BB/K003240/1)”