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Core Facilities

 

  • Bioinformatics  
  • Caption: High-throughput sequencing has greater sensitivity than microarrays to detect changes in gene expression levels.
  • We provide a data analysis and statistics consulting service to CI scientists and develop software and analysis pipelines to support high-throughput technologies.
  • High-throughput sequencing applications have continued to be a major theme for the group over the past year, with ongoing development of our analysis pipelines for ChIP-seq experiments to explore DNAprotein binding and for re-sequencing of cancer genomes to identify mutations implicated in the disease. In addition, we carried out a detailed comparison of RNAseq and oligonucleotide arrays, in which the same biological samples were analysed on both platforms for two separate studies, to support the transition from arrays to sequencing for gene expression profiling; this has influenced the design of experiments based on the newer technology as well as the bioinformatics analysis approach.
  • An important aspect of the Bioinformatics Core’s work is the development of bioinformatics infrastructure for processing sequencing data and managing the end-to-end process from sample submission to data delivery. Working with the Genomics Core, we have deployed a new commercial laboratory information management system (LIMS) to track and help manage the laboratory and bioinformatics workflows for the sequencing instruments. We continue to work closely with our colleagues in Genomics and have jointly been running weekly project review/experimental design meetings.
  • Biorepository
  • Figure 1: Total number of cell lines tested for mycoplasma at the CRUK CI, 2007–2013
  • Biorepository and cell services
  • We provide up-to-date expertise and training in all aspects of cell culture and biobanking. Our service allows simple access to storage, tracking and risk management of a variety of biological Samples.
  • Cell culture
  • Most CRUK CI laboratories use the facility and we provide basic cell culture training, a weekly mycoplasma testing service (Figure 1), a batch testing service for serum and other cell culture media components, and quality controlled bulk culture of research cell lines, including mouse embryonic fibroblasts (MEFs). We also offer a monthly routine human cell line authentication service using multiplex PCR and short tandem repeat (STR) profiling, which includes a mouse specific primer pair to detect any mouse cell contamination of human cell lines. These tests confirm integrity of research data and are becoming a requirement for publication in many leading journals, as such demand has increased.
  • We support four heavily-used Essen BioScience IncuCyte™ instruments which are compact, automated imaging platforms designed to provide kinetic, non-invasive live cell imaging. The instruments are located in a 5% CO2 incubator and acquire high definition phase contrast and fluorescent images of live, in vitro cell cultures. Custom image processing software calculates a variety of metrics, such as cell proliferation, invasion and migration assays, growth curves and optimisation of cell based assays and cell culture media components.
  • We host an annual cell culture workshop where a panel of guest experts in the field offer help and advice to our scientists.
  • We have been collaborating with the Caldas laboratory and Histopathology core facility to produce a tissue microarray consisting of 38 well-characterised breast cancer cell lines, which will be a valuable shared resource for CRUK CI scientists.
  • We have also co-authored and submitted a paper entitled “Guidelines for the use of cell lines in biomedical research”. These guidelines were prepared during 2013 by an ad hoc committee of international experts in cell biology and cell culture and are an update of the 1999 United Kingdom Coordinating Committee on Cancer Research Guidelines for the Use of Cell Lines in Cancer Research. The aim of this revised document is to highlight all major issues that might be encountered when deriving and using cell cultures for biomedical research and to provide recommendations as to how they can be identified, avoided and where possible eliminated.
  • The Human Tissue Act
  • This year saw another increase in the number of human tissue samples we received, both for general research, and clinical trials use. Our staff advise on, monitor and control the import, use, storage and disposal of human tissue samples for research, to ensure full compliance with the Human Tissue Act (2004) and the Human Tissue Authority (HTA) Codes of Practice, a statutory requirement for all research involving human tissue samples. We advise on how to request human tissue samples from the Addenbrooke’s Hospital tissue bank and other sources and how to obtain research ethics committee approval for new research projects involving the use of human tissues.
  • Future developments
  • We are exploring live cell imaging platforms, with a particular interest in imaging 3D events such as spheroid growth, cell invasion and angiogenesis. We are looking at the possibility of operating one of our IncuCyte™ instruments in hypoxic conditions, which more closely mimics the in vivo conditions of tumours. Finally, we are examining the feasibility of offering some of our current services to external Cambridge researchers.
  • Flow cytometry
    The Flow cytometry core facility provides state-of-the-art flow cytometric instrumentation, technical expertise, training, and software analysis in a collaborative environment. Our mission is to develop cytometric technologies that will best assist CI researchers in finding answers for the treatment, prevention, and understanding of cancer.

Services
Our lab offers a full range of educational and cytometric services that includes immunophenotyping, cell cycle analysis, translocation and co-localisation of cell activation markers, chromatin density, and apoptotic and necrotic analysis.  In addition we are capable of performing cell sorting for researchers so that they can isolate cell populations needed for further studies.

  • Users are offered an array of educational programs in the theory, anatomy, applications and science of flow cytometry.  Additional workshops are offered on data analysis using all of our software programs and on practical applications of current protocols in cytometry.  We also collaborate with other scientists in the Cambridge Cancer Centre on our specialised equipment.

Equipment

  • FACS Aria SORP (BD Biosciences)
    The Aria is a high-speed sorter. It is equipped with five lasers: a UV, 407nm, 445nm, 488nm, and 633nm. Our optical configuration allows us to see three UV, six violet, three indigo, six blue and three red parameters.
  • LSR II (BD Biosciences)
    The LSR II is an analytical bench top flow cytometer. It is comprised of four lasers: a UV, a violet (407nm), a blue (488 nm) and a red (633 nm). Our optical configurations allow users to see two UV, six violet, seven blue and three red fluorescent parameters.
  • FACS Caliburs (BD Biosciences)
    These flow cytometers are routinely used for phenotyping (to look at antigen, cytokine, or GFP expression), cell cycle analysis, and apoptosis studies. They are equipped with 488nm and 635nm lasers that allow users six parameter analysis.
  • ImageStream (Amnis)
    The powerful combination of quantitative image analysis and flow cytometry in a single platform creates exceptional new experimental capabilities. 405nm, 488nm and 635nm lasers for four colour/six parameter analysis as well as EDF capability for FISH analysis are available.
  • Influx Cell Sorter (BD Biosciences)
    This high speed cell sorter is contained within a biosafety cabinet to enable the isolation of cell populations from human tissue. It has four lasers at 405nm, 488nm, 561nm, 640nm and is equipped with 12 fluorescence detectors.
  • RoboSep (Stem Cell Technologies)
    This magnetic bead separator unit has customisable programs allowing positive or negative selection of virtually any cell type from any species. Up to four samples can be processed simultaneously.
  • Vi-CELL (Beckman Coulter)
    The Vi-CELL automates the widely accepted trypan blue cell exclusion method, with video imaging of the flow-through cell, to obtain results in minutes. The software conforms to key regulatory requirements with its electronic signature capability, audit trail, secure user sign on and user level permissions for clinical or preclinical studies.
  • Genome editing
    Our aim is to facilitate translational research by providing a centralised Hub for the innovation, application and use of state-of-the-art Genome Editing (GE) technologies.
    Our facility works in unison with the world-class Research Groups at the CRUK CI, and the outstanding Core facilities, to work towards truly ground breaking research and meaningful clinical impact.
    The cutting edge of Genome Editing
    There is a revolution in the field of molecular biology that is a complete game changer. With the advent of the CRISPR-Cas9 technology in 2012, Genome Editing (GE) has become simpler, cheaper and much faster than ever before. Researchers are now reinventing the way we do genetic research, being able to ask more complex and more relevant questions of biology.
     
    Our facility aims to be at the forefront of this revolution, specialising in CRISPR-Cas9 technology (as well as more established GE technologies such as viral-based GE tools). We serve as a centralised portal for the innovation, design, construction, validation, curation and housing of GE tools and resources within the CRUK CI. Furthermore, our scientists have decades of experience at applying GE technologies to a very broad range of complex, patient-relevant model systems; and of the use of these GE resources in pre-clinical experimental programmes.
    With a focus on education, we see our role as empowering Research Groups by bringing together industry and academic experts in the respective technologies, thus enabling effective knowledge exchange and network building.
     
  • Genomics
     
    Visit the Genomics core website.
    Genomics core facility
    We provide access to state-of-the-art DNA and RNA analysis instruments, methods and applications, and in particular next generation sequencing.
    Genomics has access to the latest sequencing and microarray technologies to analyse genomic data. Currently nearly all data are generated using next-generation DNA sequencing (NGS), microarrays or quantitative real-time PCR (qPCR). We have multiple Illumina NGS instruments, allowing unbiased genome-wide experiments to be performed that enable researchers to see, at base-pair resolution, what the underlying sequence differences are in cancer genomes. We are currently using commercial microarray systems from Illumina, Agilent and Affymetrix to analyse, among others: gene expression, gene copy number, methylation, and microRNA expression. Much of this work is being supplanted by NGS.
    We use two Applied Biosystems 7900s to carry out real-time PCR, mostly for lower throughput gene expression analysis but also for SNP genotyping, allelic expression and copy number. We have a Fluidigm Biomark™ instrument that allows analysis of approximately 2,000-10,000 gene expression data-points in a single run, single cell gene expression analysis and digital PCR. We use the Fluidigm Access Array™ for target enrichment and library preparation prior to NGS.
    Other technologies in the facility include the Agilent Bioanalyzer capillary electrophoresis system for QC of samples before genomic analysis, an Invitrogen Qubit® for fluorometric quantification of nucleic acids, a Covaris DNA sonicator, a Tecan Freedom EVO® robot for automated liquid handling, and Qiagen robotics for nucleic acid extraction.
    These tools in Genomics help researchers to understand the cancer genome, unravel the genetic causes of cancer and develop new methods for diagnosis and treatment. Cancer genomics has been revolutionised by NGS technology and we help CRUK CI scientists answer their research questions in this area.
    In 2013 Institute researchers showed that it is possible to sequence the exome of a tumour from circulating DNA (Murtaza et al., Nature 2013: 497; 108). Another proof-of-concept study showed that ctDNA can be used as a ‘liquid biopsy’ during the course of a patient’s treatment (Dawson et al., NEJM 2013: 368; 1199). It is likely to be several years before these technical advances become clinical tools. However, we can now sequence a cancer genome in 24 hours, last year this took five days and two years ago several weeks.
    Illumina NGS: We make extensive use of the Illumina NGS instruments, which keep the CRUK CI at the forefront of genomic research. However, the technology continues to develop and Jason Carroll’s group recently published a novel method called RIME (rapid immunoprecipitation mass spectrometry of endogenous proteins) to detect interacting proteins in ChIP complexes using NGS and mass spectrometry (Mohammed et al., Cell Rep. 2013; 3: 342).
    Microarray: Arrays continue to be used by many other groups at the CRUK CI. The Caldas group explored the differential expression of microRNAs across breast cancer subtypes in 1300 tumours using Agilent microarrays, and showed they have oncogenic and tumour-suppressive roles. (Dvinge et al., Nature. 2013; 497; 378).
    An important component of the Genomics core facility is our staff. The technologies we use are complicated and we undertake projects for the Institute’s research groups as well as training individuals to use Genomics core equipment.

INDUCTION! INDUCTION!! INDUCTION!!!

URGENT INFORMATION: This is to inform the general public that venue for the 2018 induction ceremony has been changed from the Novella Planet Hotel, Port Novo, Republic of Benin to LTV hall.  The new venue for the induction ceremony of our prestigious and reputable international professional bodies shall be Lagos State Television Combo Hall, Agidingbi, Ikeja, Lagos, Nigeria.  

Time :  12 Noon.     
Date :  May 12th,  2018.  Your presence would be highly appreciated sir/ma.