Scientific Facilities - Newcastle University

Faculty of Medical Sciences

Scientific Facilities

www.ncl.ac.uk/medicalsciences/research/facilities/

@NCLSciFaci

Scientific Facilities Newsletter: October 2016

Welcome to the Newsletter for the Faculty of Medical Sciences Scientific Facilities

In this issue: • The New Genomics Core Facility • MRCT Drug Library and High Throughput Screening • Business Voucher Scheme • NanoString nCounter Analysis Service

Forthcoming Facilities Events: • Light Microscopy Workshop • Scientific Facilities Showcase • Annual Scientific Facilities Conference

The New Genomics Core Facility This summer saw the official introduction of a new Faculty of Medical Sciences Facility, the Genomics Core Facility (GCF). Made possible by funding from the MRC’s Clinical Research Capabilities and Technology Initiative and matched funding from the Research Investment Fund, the GCF has positioned itself as • a state-of-the-art single cell genomics facility • a fully integrated next-generation sequencing core facility The GCF Team The GCF is a small team lead by Dr Jon Coxhead (SESO) supported by Raf Hussain (research technician) and Dr Rachel Queen (ESO – bioinformatics). Jon and Raf have over 15 years experience in NGS, having worked with the technology from its inception. Rachel works in partnership with the Bioinformatics Support Unit and is tasked with implementing and supporting analytical methods specific to single cell ‘omics. The GCF’s academic lead is Prof Mike Briggs. Location and Laboratory Space The Facility is open to users across the University as well as external clients, and is located on the first floor, West Wing of the Institute of Genetic Medicine. Service delivery and R&D is split across three dedicated and temperature controlled labs: pre-PCR and single cell, a post-PCR and sample QC area, and an instrument room. Please get in touch if you would like a tour! Platforms and Services The GCF offers Illumina based NGS (x2 NextSeq 500s and a MiSeq) single cell sample preparation for genomic, transcriptomic and epigenomics (Fluidigm C1). Other platforms include, Laser Capture Micro-dissection (Leica LMD7) qPCR (Fluidigm BioMark HD and BioRad CFX 96 Touch) and ddPCR (QX200 AutoDG system). All platforms are fully operational. The NGS platforms have been very popular, so far delivering ~3000 Gb sequence data since service began in March 2016. Commitment to Customers Genomic-related technologies and methods are continuously evolving, never more so than in the field of single cell research. For the GCF, the last 12 months has been focused on infrastructure investment, training and service development and delivery. Maintaining cost effective, stable, cutting edge services is best done in partnership with customer feedback. The GCF is therefore looking forward to organising workshops and establishing both a ‘user-group’ and steering committee in the coming months, and is also happy to present at your lab meeting or local seminar series! Get in touch to find out more: [email protected]

MRCT Drug Library and High Throughput Screening MRC Technology MRC Technology is an independent life science medical research charity that partners with academic, biotechnology, pharmaceutical, and charity organisations to move promising medical research forward into viable and accessible patient treatments. MRCT combine commercialisation and technology transfer/ IP management skills with diagnostic and drug discovery expertise, specialising in small molecule and therapeutic antibodies. Drug Libraries in the HTSF MRCT have supplied Newcastle University’s High Throughput Screening Facility (HTSF) with 20,000 compounds for research use. This complements the existing siRNA library held by the HTSF. For further information on running a screen with either the MRCT drug library or the siRNA library, please contact [email protected].

Business Voucher Scheme Newcastle University’s Business Voucher Scheme is designed to encourage interactions with UK business and other organisations, by supporting projects that will enable long-term, mutually beneficial collaborations. Organisations may be eligible for up to £5,000 of matched funding towards a range of University services, including accessing our Facilities. Find out more about the Business Voucher Scheme, or for more information please contact Linda Wilson ([email protected]).

NanoString nCounter Analysis Service

What is NanoString Technology? The NanoString nCounter analysis system is the first and only platform that can deliver direct profiling of individual molecules in a highly multiplexed single reaction without any need for amplification. Critically, NanoString technology is superior to any other current RNA analysis technique for FFPE-derived material. This protocol provides digital readouts of relative gene expression from hundreds of cDNA, mRNA, and miRNA fragments from extracted nucleic acids, FFPE material, and whole cell lysate, whilst obviating any enzymatic reactions that may introduce bias in the results.

About our Service • Based in the Human Dendritic Cell Lab, Newcastle University Medical School • Technician-run service with specialist advice available • Open to both internal and external users • Turnaround time for samples – approximately 10 working days • Newcastle University users can receive a 10% discount on NanoString consumables by quoting “Newcastle NanoString” when placing the order

Benefits of using the nCounter Platform • Ability to measure 20 to 800+ genes in a single reaction • Digitally detect and analyse samples in a fully automated manner • No signal amplification or polymerase steps required • High flexibility of sample input (including FFPE samples)

Get in Touch For more information about the technology, please visit the NanoString website, or for further details about the Newcastle University NanoString System and its use, please contact: • Anastasia Resteu ([email protected]) • Kile Green ([email protected] - until December 2016)

Forthcoming Facilities Events Light Microscopy Workshop 8-10 November 2016 Taking place over three days with a mixture of taught and hands-on workshops, this popular imaging workshop aims to provide a grounding in microscopy and fluorescent imaging techniques. Find out more and register via the BioImaging Unit website For further information please contact [email protected]

Scientific Facilities Showcase 9.00 - 12.00, Thursday 17 November 2016, Baddiley-Clark Seminar Room Informal, drop-in style event with refreshments available. Meet the staff from our Core Scientific Facilities and find out how to access their expertise and equipment. Please register at go.ncl.ac.uk/showcase2016

Annual Scientific Facilities Conference Practicalities of Cellular Analysis: Understanding the Cell, Piece by Piece Tuesday 28 March 2017, Newcastle University Medical School Our 2017 Scientific Facilities Conference will be centered around cellular analysis and the techniques and expertise relating to Bioimaging, Electron Microscopy, Flow Cytometry, and Preclinical In Vivo Imaging. Visit the conference website for more information, including registration and sponsorship options. New this year: Submit an abstract for the Poster Presentation Session. https://conferences.ncl.ac.uk/practicalities2017/

#Practicalities2017