NUCLEUS Genomics

NUCLEUS Genomics

Nucleus Genomics Facility

NUCLEUS Genomics is a state of the art core facility, forming part of the University of Leicester's Core Biotechnology Services (CBS).  We enable researchers both within, and outside the University, to incorporate the very latest Genomics technologies in their experiments.

The facility is equipped with various state-of-the-art platforms:

Next Generation Sequencing Platforms: Illumina Miseq, Oxford Nanopore MinION

10X Genomics Chromium Controller

Microarray Scanners: Illumina iscan and Agilent C-scanner

High throughput quantitative PCR platforms: Roche Light Cycler, ABI 7900HT

Systems for QC: Nanodrop (ND8000 - 8 channel), Fluorescent Nanodrop (single channel), Agilent Bioanalyser

Projects can be handed over to the NUCLEUS team for completion, or conducted in some form of collaboration with the users. To enable this, a support model has been devised that also involves training and laboratory hotel activities.

The facility is a non-profit academic lab. Our customers are charged on a cost recovery basis. Pricing for our systems is provided for guidance (See charges page).

For a quotation, or for additional information, please contact us:

Dr Nicolas Sylvius or Reshma Vaghela.

 

Select Publications

Mitigating the effects of reference sequence bias in single-multiplex massively parallel sequencing of the mitochondrial DNA control region.

Huszar TI, Wetton JH, Jobling MA. Forensic Sci Int Genet. 2019 Jan 16;40:9-17

 

A phylogenetic framework facilitates Y-STR variant discovery and classification via massively parallel sequencing

Huszar TI, Jobling MA, Wetton JH. Forensic Sci Int Genet. 2018 Jul;35:97-106

 

SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells.

Toghill BJ, Saratzis A, Freeman PJ, Sylvius N, UKAGS collaborators, Bown MJ. Clinical Epigenetics, 2018 Mar 2;10:29

 

Adaptive and Behavioral Changes in Kynurenine 3-Monooxygenase Knockout Mice: Relevance to Psychotic Disorders.

Erhardt S, Pocivavsek A, Repici M, Liu XC, Imbeault S, Maddison DC, Thomas MAR, Smalley JL, Larsson MK, Muchowski PJ, Giorgini F, Schwarcz R. Biol Psychiatry. 2017 Nov 15;82(10):756-765

 

Impaired P2X1 Receptor-Mediated Adhesion in Eosinophils from Asthmatic Patients.

Wright A, Mahaut-Smith M, Symon F, Sylvius N, Ran S, Bafadhel M, Muessel M, Bradding P, Wardlaw A, Vial C. J Immunol. 2016 May 9. pii: 1501585. [Epub ahead of print]

 

Microarray-based Gene Expression Profiling of Abdominal Aortic Aneurysm.

Butt HZ, Sylvius N, Salem MK, Wild JB, Dattani N, Sayers RD, Bown MJ. Eur J Vasc Endovasc Surg. 2016 May 2. pii: S1078-5884(16)00173-8. doi: 10.1016/j.ejvs.2016.03.016. [Epub ahead of print]

 

Variation in Inflammatory Response during Pneumococcal Infection Is Influenced by Host-Pathogen Interactions but Associated with Animal Survival.

Jonczyk MS, Escudero L, Sylvius N, Norman M, Henriques-Normark B, Andrew PW. Infect Immun. 2016 Mar 24;84(4):894-905. doi: 10.1128/IAI.01057-15. Print 2016 Apr.

 

Identification of microRNAs associated with abdominal aortic aneurysms and peripheral arterial disease.

Stather PW, Sylvius N, Sidloff DA, Dattani N, Verissimo A, Wild JB, Butt HZ, Choke E, Sayers RD, Bown MJ. Br J Surg. 2015 Jun;102(7):755-66. doi: 10.1002/bjs.9802. Epub 2015 Apr 2

 

Genetic factors regulating lung vasculature and immune cell functions associate with resistance to pneumococcal infection.

Jonczyk MS, Simon M, Kumar S, Fernandes VE, Sylvius N, Mallon AM, Denny P, Andrew PW. PLoS One. 2014 Mar 3;9(3):e89831. doi: 10.1371/journal.pone.0089831. eCollection 2014

 

Differential microRNA expression profiles in peripheral arterial disease.

Stather PW, Sylvius N, Wild JB, Choke E, Sayers RD, Bown MJ. Circ Cardiovasc Genet. 2013 Oct;6(5):490-7. (With the department of Cardiovascular Sciences, University of Leicester)

 

MicroRNAs associated with the pathways involved in the pathogenesis of abdominal aortic aneurysms.

P.W. Stathera, J.B. Wild, N. Sylvius, E. Choke, R.D. Sayers, M.J. Bown. Artery Research, Volume 7, Issue 1, March 2013, Pages 28–35. (With the department of Cardiovascular Sciences, University of Leicester)

 

Low density lipoprotein receptor related protein 1 and abdominal aortic aneurysms.

Wild JB, Stather PW, Sylvius N, Choke E, Sayers RD, Bown MJ. Eur J Vasc Endovasc Surg. 2012 Aug;44(2):127-32. (With the department of Cardiovascular Sciences, University of Leicester)

 

A mechanistic basis for amplification differences between samples and between genome regions.

Veal CD, Freeman PJ, Jacobs K, Lancaster O, Jamain S, Leboyer M, Albanes D, Vaghela RR, Gut I, Chanock SJ, Brookes AJ. BMC Genomics. 2012 Sep 5;13:455.

 

Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1.

Bown MJ, Jones GT, Harrison SC, Wright BJ, Bumpstead S, Baas AF, Gretarsdottir S, Badger SA, et al. Am J Hum Genet. 2011 Nov 11;89(5):619-27. (With the department of Cardiovascular Sciences, University of Leicester)

 

MicroRNA expression profiling in patients with lamin A/C associated muscular dystrophy.

Sylvius N, Bonne G, Straatman k, Reddy T, Gant TW, Shackleton S. FASEB J. 2011 Nov;25(11):3966-78. (With the department of Biochemistry, University of Leicester)

 

The Kynurenine Pathway Modulates Neurodegeneration in a Drosophila Model of Huntington's Disease.

Campesan S, Green EW, Breda C, Sathyasaikumar KV, Muchowski PJ, Schwarcz R, Kyriacou CP, Giorgini F. Curr Biol. 2011 Jun 7;21(11):961-6. (With the department of Genetics, University of Leicester)

 

Pathway analysis shows association between FGFBP1 and hypertension.

Tomaszewski M, Charchar FJ, Nelson CP, Barnes T, Denniff M, Kaiser M, Debiec R, et al. J Am Soc Nephrol. 2011 May;22(5):947-55. (With the department of Cardiovascular Sciences)

 

Dense genotyping of candidate gene Loci identifies variants associated with high-density lipoprotein cholesterol.

Edmondson, AC, Braund PS, Stylianou IM, Khera AV, Nelson CP, Wolfe ML, Derohannessian SL. et al. Circ Cardiovasc Genet. 2011 Apr;4(2):145-55. (With the department of Cardiovascular Sciences, University of Leicester)

 

Heritability of early repolarization: a population-based study.

Reinhard W, Kaess BM, Debiec R, Nelson CP, Stark K, Tobin MD, Macfarlane PW et al. Circ Cardiovasc Genet. 2011 Apr;4(2):134-8. (With the department of Cardiovascular Sciences, University of Leicester)

 

Functional gene expression profiling in yeast implicates translational dysfunction in mutant huntingtin toxicity.

Tauber E, Miller-Fleming L, Mason RP, Kwan W, Clapp J, Butler NJ, Outeiro TF, Muchowski PJ, Giorgini F. J Biol Chem. 2011 Jan 7;286(1):410-9. (With the department of Genetics, University of Leicester)

 

Large-scale candidate gene analysis of HDL particle features.

Kaess BM, Tomaszewski M, Braund PS, Stark K, Rafelt S, Fischer M, Hardwick R, et al. PLoS One. 2011 Jan 21;6(1):e14529. (With the department of Cardiovascular Sciences, University of Leicester)

 

Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height.

Lanktree MB, Guo Y, Murtaza M, Glessner JT, Bailey SD, Onland-Moret NC, Lettre G, et al. Am J Hum Genet. 2011 Jan 7;88(1):6-18. (With the department of Health Sciences and the department of Cardiovascular Sciences, University of Leicester)

 

The relationship between plasma angiopoietin-like protein 4 levels, angiopoietin-like protein 4 genotype, and coronary heart disease risk.

Smart-Halajko MC, Robciuc MR, Cooper JA, Jauhiainen M, Kumari M, Kivimaki M, Khaw KT, et al. Arterioscler Thromb Vasc Biol. 2010 Nov;30(11):2277-82. (With the department of Cardiovascular Sciences, University of Leicester)

 

Lysine Specific Demethylase 1 (LSD1) Regulates the Embryonic Transcriptome and CoREST Stability.

Foster CT, Dovey OM, Lezina L, Luo JL, Gant TW, Barlev N, Bradley A, Cowley SM. Mol Cell Biol. 2010 Aug 16. [Epub ahead of print]. (With the department of Biochemistry, University of Leicester)

 

Histone deacetylase 1 (HDAC1), but not HDAC2, controls embryonic stem cell differentiation.

Dovey OM, Foster CT, Cowley SM. Proc Natl Acad Sci U S A. 2010 May 4; 107(18):8242-7. (With the department of Biochemistry, University of Leicester)

 

Genetic Architecture of Ambulatory Blood Pressure in the General Population: Insights From Cardiovascular Gene-Centric Array.

Tomaszewski M, Debiec R, Braund PS, Nelson CP, Hardwick R, Christofidou P et al. Hypertension. 2010 Dec;56(6):1069-1076. Epub 2010 Nov 8. (With the department of Cardiovascular Sciences, University of Leicester)

 

Triglyceride-mediated pathways and coronary disease: collaborative analysis of 101 studies.

Triglyceride Coronary Disease Genetics Consortium and Emerging Risk Factors Collaboration, Sarwar N, Sandhu MS, Ricketts SL, Butterworth AS, Di Angelantonio E, Boekholdt SM et al. Lancet. 2010 May 8;375(9726):1634-9. (With the department of Cardiovascular Sciences, University of Leicester)

 

 

 

 

 

Nucleus Tech Notes and Protocols

1/ Maxwell Promega RNA extraction - Simplified protocol

2/  Bioanalyzer Guidance and Kit Information.pdf

3/  Consequences of Various Contaminants on RNA Quantification and Quality Controls

Consequences_RNA_degradation_Bioanalyzer_Trace.pdf

Through the RNA isolation procedure, RNA samples are often degraded or contaminated by reagents carried over such as TRIzol, ethanol, proteins or genomic DNA. Here we provide examples and analysis of the consequences of these contaminants on the parameters usually checked in RNA quality control such as the RIN number on the bioanalyzer and the 260/280 ratio on a nanodrop or spectrophotmeter.

 4/  targetamp---nano-labeling-kit-for-illumina-expression-beadchip-.pdf

 

 

Terms and Conditions

Projects handed over to the Genomics Facility

 

1/ Projects are quoted on a case by case basis in order to adapt to the specific requirements of each customer. Reagents are ordered once the customer has agreed with our quotation and our conditions of use. For non-collaborative work with external customers, we require prepayment (usually 10%) and the establishment of a service contract between the customer and the University of Leicester before we start the work. Once the work is completed, data are supplied after the final payment is made. For costly projects, customers may be asked to cover the cost of the reagents upfront. Customers have to bear in mind that analytical work on biological samples often results in a certain percentage of failure due to reasons beyond anybody’s control. We estimate to 5-10% the number of samples failing and requiring reruns. The customer will have to budget the cost of reruns if needed.

 

2/ The service offering and commitment described in our quotations are conditional upon the quality and amount of samples supplied by the customer. RNA or DNA samples directly provided by the customer are always assessed. If some samples do not pass the quality controls, the customer will be asked whether she/he wants us to proceed with them. Should she/he decide not to proceed, we will still have to charge the cost of the sample quality control. Should she/he decide to proceed, we will not be held liable for failure of the experiments.

 

3/ We are usually not able to commit to any specific delivery deadlines. However, we do our best to complete all projects within a reasonable timeframe, for example, 2-4 weeks for a small to middle scale project (< 100 samples). However, this may vary depending on the workload in our services at the time we receive the samples and the reagents. We provide the customer with a more accurate time plan once we have the samples and an estimated shipping date of the reagents.

 

4/ The facility reserves the right to recycle or dispose of any unclaimed samples and kits/reagents after one year without prior notice.

 

5/ The staff of the Genomics Facility do not provide reports on completed work to any customer other than the one who commissioned the work.

Charges

 

Charges can vary considerably even on the same platform for different protocols and project types. We advise all potential users to contact us at an early stage in their experimental design so that we can produce accurate quotes and discuss available options. The table below provides guidance on our charges. If training is needed an additional charge applies.

Technology Typical Charge
Robotics Biomek FX/2000 £30 per hour/£100 half day use
Sample preparation Bioruptor Sonicator No charge
Next Generation Sequencing Illumina Miseq Prices depends on application. Contact us for quotation
Next Generation Sequencing Oxford Nanopore Minion Prices depends on application. Contact us for quotation
Microarray Agilent C-scanner Prices depend on the cost of microarrays and application. Contact us for quotation
Microarray GenePix Scanne £20 per hour (discounts available for multiple runs)
Microarray Illumina Iscan Prices depend on the cost of microarrays and application. Contact us for quotation
Quantitative Real-time PCR ABI7900HT £20 per run
Quantitative Real-time PCR Roche LightCycler 480 £20 per run
digital PCR Bio-Rad QX200 To be announced
DNA/RNA purification Promega Maxwell About £7 to £8 per sample depending on the application
DNA/RNA quality check Agilent Bioanalyzer £25-£40 per run depending on the chips
DNA/RNA quality check NanoDrop 3300 Fluoroscent spectrometer Free for users of our NGS, microarray platforms or qPCR platforms
DNA/RNA quality check NanoDrop 8000 Spectrophotometer Free for users of our NGS, microarray platforms or qPCR platforms

Contact NUCLEUS Genomics

Dr Nicolas Sylvius (Research Associate)

Reshma Vaghela (Experimental Officer)

NUCLEUS
Genomics Core Facility
The Centre for Core Biotechnology Services (CBS)
University of Leicester
Adrian Building
University Road
Leicester
LE1 7RH
UK

Fax: +44(0)116 252 3378
Tel: +44(0)116 252 3365

Sample_Submission_Form.xlsx

application/vnd.openxmlformats-officedocument.spreadsheetml.sheet icon Sample_Submission_Form.xlsx — application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, 11 kB (11533 bytes)

Share this page:

Contact NUCLEUS

Dr Nicolas Sylvius
(Research Associate)

Reshma Vaghela
(Research Technician)

NUCLEUS
Genomics Core Facility
Department of Genetics
University of Leicester
Adrian Building
University Road
Leicester
LE1 7RH
UK

Fax: +44(0)116 252 3378
Tel: +44(0)116 252 3365/3375