University of Edinburgh
Lee Murphy
Wellcome Trust Clinical Research Facility
Western General Hospital
Edinburgh EH4 2XU
https://clinical-research-facility.ed.ac.uk/core-services/genetics
RRID: RRID:SCR_025433
Illumina iScan System
Can scan thousands of array samples per day, without sacrificing data quality or reproducibility. [Product Link]
RRID:SCR_020128
Illumina iSeq 100 Sequencing System
Makes next generation sequencing easier. Designed for simplicity, it allows labs of all sizes to sequence DNA and RNA at push of button. [Product Link]
RRID:SCR_020125
Illumina NextSeq 1000 and NextSeq 2000 Sequencing Systems
Benchtop sequencers that allow you to explore new science across variety of current and emerging applications, with higher efficiency and fewer restraints. [Product Link]
RRID:SCR_020140
Life Technologies QuantStudio 5 Real Time PCR System
Carry out rapid food protection testing with the Applied Biosystems QuantStudio 5 Food Safety Real-Time PCR System. The and easy-to-use system is best for users who need superior performance, maximum dye versatility, and security options in a real time PCR system. The QuantStudio5 Food Safety System is a high performance benchtop platform combining ease-of-use and system connectivity. Benefit from the flexibility of a 6-channel, 96-well, cloud-enabled open platform suitable for running our full range of PCR solutions for food safety, authenticity, and quality testing. [Product Link]
RRID:SCR_020240
Perkin Elmer Chemagic 360 Genetic isolation Workstation
Nucleic Acid Extractor for Medium to High Throughput. Based on our patented chemagen magnetic bead technology the chemagic 360 instrument represents the best solution for nucleic acid isolation in a huge variety of research market segments including but not limited to Biobanking/Human Genetics, HLA Typing, Virus and Bacteria Detection. Experience the revolutionary compact benchtop design of our newly developed chemagic 360 Nucleic Acid Extractor. Based on the well-established chemagen Technology, the system offers a flexible solution for different sample processing and throughput needs. Configurable with three kinds of chemagic Rod Heads (see table below) the system can process sample volumes from 10 ?l 10 ml. [Product Link]
RRID:SCR_020394
(Equipment No Longer Active At this Facility)
Element AVITI24
Short-read sequencing platform
Element AVITI24 Sequencing System
Sequencing system
(Equipment No Longer Active At this Facility)
ONT PromethION24
Long-read single-molecule sequencer
ONT PromethION24 Sequencing System
Long-read single-molecule sequencing system
(Equipment No Longer Active At this Facility)
PacBio Revio
Long-read sequencing platform
PacBio Revio Sequencing System
Long-readd sequencing system
Stilla Naica Digital PCR platform
Digital PCR platform
AVITI Sequencing
Digital PCR
DNA Analysis
DNA Isolation
Genomics
Genotyping
Illumina Short-read Sequencing
Methylation Analysis
ONT Sequencing
PacBio Revio Sequencing
RNA Analysis
RNA Isolation
1.) Vancaester E, Oldrieve GR, Reid A, Koutsovoulos G, Laetsch DR, Makepeace BL, Tanya V, Poppert S, Krücken J, Wolstenholme A, Blaxter M (2025 Dec 10). Ghosts of symbionts past: the hidden history of the dynamic association between filarial nematodes and their Wolbachia endosymbionts. G3 (Bethesda, Md.), 15(12), . . PMID: 41030195.
2.) Durmaz Mitchell E, Kerdaffrec E, Schmidt P, Flatt T, Kittelmann S (2025 Sep 1). A Balanced Inversion Polymorphism Exhibits a Dominance Reversal at the Gene Expression Level that Depends on Developmental Context. Molecular biology and evolution, 42(9), . . PMID: 40884829.
3.) Chybowska AD, Bernabeu E, Yousefi P, Suderman M, Hillary RF, Clark R, MacGillivray L, Murphy L, Harris SE, Corley J, Campbell A, Spires-Jones TL, McCartney DL, Cox SR, Price JF, Evans KL, Marioni RE (2025 Apr 4). A blood- and brain-based EWAS of smoking. Nature communications, 16(1), 3210. . ID: 40180905.
4.) Boardman JP, Andrew R, Bastin ME, Battersby C, Batty GD, Cábez MB, Cox SR, Hall J, Ingledow L, Marioni RE, Modi N, Murphy L, Quigley AJ, Reynolds RM, Richardson H, Stock SJ, Thrippleton MJ, Tsanas A, Whalley HC (2024 Sep 16). Preterm birth as a determinant of neurodevelopment and cognition in children (PRENCOG): protocol for an exposure-based cohort study in the UK. BMJ open, 14(9), e085365. . ID: 39284691.
5.) Tijjani A, Kambal S, Terefe E, Njeru R, Ogugo M, Ndambuki G, Missohou A, Traore A, Salim B, Ezeasor C, D'andre H C, Obishakin ET, Diallo B, Talaki E, Abdoukarim IY, Nash O, Osei-Amponsah R, Ravaorimanana S, Issa Y, Zegeye T, Mukasa C, Tiambo C, Prendergast JGD, Kemp SJ, Han J, Marshall K, Hanotte O (2024 Jul 19). Genomic Reference Resource for African Cattle: Genome Sequences and High-Density Array Variants. Scientific data, 11(1), 801. . PMID: 39030190.
6.) Mckinnon K, Conole ELS, Vaher K, Hillary RF, Gadd DA, Binkowska J, Sullivan G, Stevenson AJ, Corrigan A, Murphy L, Whalley HC, Richardson H, Marioni RE, Cox SR, Boardman JP (2024 Jun 29). Epigenetic scores derived in saliva are associated with gestational age at birth. Clinical epigenetics, 16(1), 84. . ID: 38951914.
7.) McDonnell E, Orr SE, Barter MJ, Rux D, Brumwell A, Wrobel N, Murphy L, Overmann LM, Sorial AK, Young DA, Soul J, Rice SJ (2024 May 6). Epigenetic mechanisms of osteoarthritis risk in human skeletal development. medRxiv : the preprint server for health sciences, (), . . ID: 38766055.
8.) Chybowska AD, Gadd DA, Cheng Y, Bernabeu E, Campbell A, Walker RM, McIntosh AM, Wrobel N, Murphy L, Welsh P, Sattar N, Price JF, McCartney DL, Evans KL, Marioni RE (2024 Feb). Epigenetic Contributions to Clinical Risk Prediction of Cardiovascular Disease. Circulation. Genomic and precision medicine, 17(1), e004265. . ID: 38288591.
9.) Hillary RF, McCartney DL, Smith HM, Bernabeu E, Gadd DA, Chybowska AD, Cheng Y, Murphy L, Wrobel N, Campbell A, Walker RM, Hayward C, Evans KL, McIntosh AM, Marioni RE (2023 Jul). Blood-based epigenome-wide analyses of 19 common disease states: A longitudinal, population-based linked cohort study of 18,413 Scottish individuals. PLoS medicine, 20(7), e1004247. . ID: 37410739.
10.) Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, L (2023 Jul). Author Correction: GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature, 619(7971), E61. . ID: 37433877.
11.) Gillan JL, Chokshi M, Hardisty GR, Clohisey Hendry S, Prasca-Chamorro D, Robinson NJ, Lasota B, Clark R, Murphy L, Whyte MKB, Baillie JK, Davidson DJ, Bao G, Gray RD (2023 May 26). CAGE sequencing reveals CFTR-dependent dysregulation of type I IFN signaling in activated cystic fibrosis macrophages. Science advances, 9(21), eadg5128. . ID: 37235648.
12.) Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, L (2023 May). GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Nature, 617(7962), 764-768. . ID: 37198478.
13.) Cheng Y, Gadd DA, Gieger C, Monterrubio-Gómez K, Zhang Y, Berta I, Stam MJ, Szlachetka N, Lobzaev E, Wrobel N, Murphy L, Campbell A, Nangle C, Walker RM, Fawns-Ritchie C, Peters A, Rathmann W, Porteous DJ, Evans KL, McIntosh AM, Cannings TI, Waldenberger M, Ganna A, McCartney DL, Vallejos CA, Marioni RE (2023 Apr). Development and validation of DNA methylation scores in two European cohorts augment 10-year risk prediction of type 2 diabetes. Nature aging, 3(4), 450-458. doi: 10.1038/s43587-023-00391-4. ID: 37117793.
14.) Kousathanas A, Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, Shen X, Elliott KS, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Wang B, Rhodes D, Klaric L, Zechner M, Parkinson N, Siddiq A, Goddard P, Donovan S, Maslove D, Nichol A, Semple MG, Zainy T, Maleady-Crowe F, Todd L, Salehi S, Knight J, Elgar G, Chan G, Arumugam P, Patch C, Rendon A, Bentley D, Kingsley C, Kosmicki JA, Horowitz JE, Baras A, Abecasis GR, Ferreira MAR, Justice (2022 Jul). Whole-genome sequencing reveals host factors underlying critical COVID-19. Nature, 607(7917), 97-103. . ID: 35255492.
15.) Robertson NA, Latorre-Crespo E, Terradas-Terradas M, Lemos-Portela J, Purcell AC, Livesey BJ, Hillary RF, Murphy L, Fawkes A, MacGillivray L, Copland M, Marioni RE, Marsh JA, Harris SE, Cox SR, Deary IJ, Schumacher LJ, Kirschner K, Chandra T (2022 Jul). Longitudinal dynamics of clonal hematopoiesis identifies gene-specific fitness effects. Nature medicine, 28(7), 1439-1446. . ID: 35788175.
16.) Cunningham-Burley S, McCartney DL, Campbell A, Flaig R, Orange CEL, Porteous C, Aitken M, Mulholland C, Davidson S, McCafferty SM, Murphy L, Wrobel N, McCafferty S, Wallace K, StClair D, Kerr S, Hayward C, McIntosh AM, Sudlow C, Marioni RE, Pell J, Miedzybrodzka Z, Porteous DJ (2022). Feasibility and ethics of using data from the Scottish newborn blood spot archive for research. Communications medicine, 2(), 126. . ID: 36210800.
17.) Wickenhagen A, Sugrue E, Lytras S, Kuchi S, Noerenberg M, Turnbull ML, Loney C, Herder V, Allan J, Jarmson I, Cameron-Ruiz N, Varjak M, Pinto RM, Lee JY, Iselin L, Palmalux N, Stewart DG, Swingler S, Greenwood EJD, Crozier TWM, Gu Q, Davies EL, Clohisey S, Wang B, Trindade Maranhão Costa F, Freire Santana M, de Lima Ferreira LC, Murphy L, Fawkes A, Meynert A, Grimes G, Da Silva Filho JL, Marti M, Hughes J, Stanton RJ, Wang ECY, Ho A, Davis I, Jarrett RF, Castello A, Robertson DL, Semple MG, Open (2021 Oct 29). A prenylated dsRNA sensor protects against severe COVID-19. Science (New York, N.Y.), 374(6567), eabj3624. . ID: 34581622.
18.) Pairo-Castineira E, Clohisey S, Klaric L, Bretherick AD, Rawlik K, Pasko D, Walker S, Parkinson N, Fourman MH, Russell CD, Furniss J, Richmond A, Gountouna E, Wrobel N, Harrison D, Wang B, Wu Y, Meynert A, Griffiths F, Oosthuyzen W, Kousathanas A, Moutsianas L, Yang Z, Zhai R, Zheng C, Grimes G, Beale R, Millar J, Shih B, Keating S, Zechner M, Haley C, Porteous DJ, Hayward C, Yang J, Knight J, Summers C, Shankar-Hari M, Klenerman P, Turtle L, Ho A, Moore SC, Hinds C, Horby P, Nichol A, Maslove D (2021 Mar). Genetic mechanisms of critical illness in COVID-19. Nature, 591(7848), 92-98. doi: 10.1038/s41586-020-03065-y. ID: 33307546.
19.) Masalmeh RHA, Taglini F, Rubio-Ramon C, Musialik KI, Higham J, Davidson-Smith H, Kafetzopoulos I, Pawlicka KP, Finan HM, Clark R, Wills J, Finch AJ, Murphy L, Sproul D (2021 Jan 29). De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG islands. Nature communications, 12(1), 694. . ID: 33514701.
20.) Keag OE, Murphy L, Bradley A, Deakin N, Whyte S, Norman JE, Stock SJ (2020). Postal recruitment for genetic studies of preterm birth: A feasibility study. Wellcome open research, 5(), 26. . ID: 32322692.
21.) Walker RM, MacGillivray L, McCafferty S, Wrobel N, Murphy L, Kerr SM, Morris SW, Campbell A, McIntosh AM, Porteous DJ, Evans KL (2019). Assessment of dried blood spots for DNA methylation profiling. Wellcome open research, 4(), 44. . ID: 30984878.
22.) Habota T, Sandu AL, Waiter GD, McNeil CJ, Steele JD, Macfarlane JA, Whalley HC, Valentine R, Younie D, Crouch N, Hawkins EL, Hirose Y, Romaniuk L, Milburn K, Buchan G, Coupar T, Stirling M, Jagpal B, MacLennan B, Priba L, Harris MA, Hafferty JD, Adams MJ, Campbell AI, MacIntyre DJ, Pattie A, Murphy L, Reynolds RM, Elliot R, Penton-Voak IS, Munafò MR, Evans KL, Seckl JR, Wardlaw JM, Lawrie SM, Haley CS, Porteous DJ, Deary IJ, Murray AD, McIntosh AM (2019). Cohort profile for the STratifying Resilience and Depression Longitudinally (STRADL) study: A depression-focused investigation of Generation Scotland, using detailed clinical, cognitive, and neuroimaging assessments. Wellcome open research, 4(), 185. . ID: 35237729.
23.) McRae AF, Marioni RE, Shah S, Yang J, Powell JE, Harris SE, Gibson J, Henders AK, Bowdler L, Painter JN, Murphy L, Martin NG, Starr JM, Wray NR, Deary IJ, Visscher PM, Montgomery GW (2018 Dec 4). Identification of 55,000 Replicated DNA Methylation QTL. Scientific reports, 8(1), 17605. . ID: 30514905.
The University of Edinburgh Genomics Core provides platforms and technical expertise to support internal, external and commercial research projects requiring DNA & RNA extraction, microarrays, genotyping and sequencing.
