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Genomics and Genome Engineering Core Facility

The Genomics and Genome Engineering Core Facility provides infrastructure with access to state-of-the-art genomics equipment, NGS library preparation, and affordable genome engineering services.

The Facility is supported by experienced specialists who can offer their expertise and support at all stages of the research project. We can help with experimental design, providing technical services and training to facilitate your research projects requiring genomics and/or genome engineering technologies.

We provide comprehensive sequencing services including next-generation sequencing (NGS) library preparation and sequencing using the Illumina HiSeq 2500 and MiSeq. We work closely with the Bill Lyons Informatics Centre (BLIC), based at the UCL Cancer Institute, who can provide help and support with sequencing data analysis for various applications.

Our genome engineering services include production and use of the latest CRISPR technologies as well as banking and distribution of associated in-house developed CRISPR reagents. We have the Human and Mouse Open Biosystems GIPZ shRNAmir lentiviral libraries which can be purchased as individual hairpins or as pooled libraries for multiplexing screening. The Facility provides support in assay design and use of the RNAi libraries collections. 

We currently offer a Miseq service for sequencing edited cell populations or single cell clones. Please contact us for more information about this service.


Equipment

There are a number of high throughput Genomics platforms available within the Facility. We are happy to undertake projects for the research groups based within the Cancer Institute as well as UCL and also provide training to researchers who would like to use our Facility equipment.

Please contact Pawan Dhami (p.dhami@ucl.ac.uk) to discuss your project and training requirements and costs.

Book Equipment Here

HiSeq 2500

Location: Lab 228

The Illumina HiSeq 2500 is a powerful and scalable high-throughput sequencing system that supports a wide range of applications ensuring high quality data. The system offers the flexibility of two run modes – Rapid Run (2 lane flow cell) and High Output Run (8 lane flow cell) mode to fit different project needs. Furthermore, it is possible to run one flow cell on its own or two flow cells simultaneously.

Book Here

MiSeq

Location: Lab 228

The Illumina MiSeq is a highly automated benchtop sequencing system suitable for a wide range of applications such as Small genomes sequencing, Targeted resequencing, Small RNA sequencing, Metagenome sequencing, de novo transcriptome sequencing and more. It is fast and cost-effective with short sequencing run times and long reads while maintaining high data quality.

Book Here

Fluidigm C1 Single-cell Auto Prep System

Location: Lab G25

The Fluidigm C1 is a microfluidic, automated platform for single-cell genomics research. The system enables the isolation of single cells from cellular suspensions and preparation of single-cell templates for mRNA sequencing, DNA sequencing, miRNA expression or Epigenetics. The system uses Integrated Fluidic Circuit (IFC) chips to capture cells depending on the size of the cells and are available in 5-10 microns, 10-17 microns or 17-25 microns size ranges. The standard IFC has the capacity to capture and prepare libraries from up to 96 single cells. The HT (high-throughput) IFC provides mRNA quantification for up to 800 cells.

Book Here

nCounter SPRINT System

Location: Lab 303B

The nCounter SPRINT system from Nanostring Technologies utilizes a digital barcode technology for direct multiplexed measurement of nucleic acids with high levels of precision and sensitivity. The technology uses fluorescent labelled reporter probes called ‘codesets’ that bind to the target molecules and single molecule imaging to detect and count hundreds of molecules in a single reaction (<1 copy per cell). Pre-designed Codesets are available for mRNA, DNA and miRNA and custom Codesets can be designed. The major advantage of the technology is the ability to analyse RNA samples of poor quality such as FFPE (formalin-fixed, paraffin-embedded) samples.

Book Here

QX200 Droplet Digital PCR System

Location: Lab 205

The QX200 Droplet Digital (ddPCR) System provides absolute quantification of target DNA or RNA molecules for dye (EvaGreen) or probe-based (TaqMan) digital PCR applications. The method involves partitioning ddPCR reaction mix into thousands of nanolitre-sized droplets. After PCR on a thermal cycler, the droplets from each sample are analysed individually on the QX200 Droplet Reader. Up to 96 samples can be run at a time.

ThunderStorm NGS Target Enrichment System

Location: Lab G09

The RainDance ThunderStorm System is an automated high-throughput targeted sequencing platform that utilizes RainDance’s single molecule PCR technology that generates millions of unique microdroplet PCR reactions and targets up to 20,000 genomic loci in a single sample. It can process up to 96 samples and use as little as 250ng of unamplified genomic DNA. RainDance’s Tailed Primer Assay enables integration of sequencing adaptors directly into sequence-ready targets, thus eliminating the need for downstream NGS library preparation.

QuantStudio 5 Real-Time PCR System

Location: Lab 303C

The QuantStudio 5 Real-Time PCR System is designed for users who need a high performance instrument with features for maximum experiment control. The instrument as well as the Design and Analysis software are very easy to use.

Book Here

Eppendorf MasterCycler RealPlex qPCR Instruments

Location: Lab 303C

We have three Mastercycler RealPlex instruments from Eppendorf which are compact, easy to use and flexible platforms to obtain accurate, consistent and reproducible results. The instruments are compatible with plates and reagents from different companies which make these an ideal and flexible platform to use.

Book Here

Agilent 2100 Bioanalyzer Instrument

Location: Lab 303C

The Agilent 2100 Bioanalyzer provides sizing, quantification and purity assessments for DNA, RNA and protein samples. Kits for the following assays are kept in stock by the Facility – RNA nano, DNA 1000 and DNA High Sensitivity.

Book Here

Qubit 3.0 Fluorometer

Location: Lab 228

The Qubit 3.0 Fluorometer is an extremely simple to use benchtop fluorometer that can be used for the quantitation of DNA, RNA, microRNA and protein using the highly sensitive and accurate fluorescence-based Qubit quantitation assays. Use of dyes that are selective for dsDNA, RNA or protein minimizes the effects of contaminants in the sample. Data can be easily exported to a USB drive.

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Tapestation 2200

There is a Tapestation available in the Pathology Core Facility. Please see the Pathology Core Facility page for further details and booking.

Genomics Services

NGS library preparation

We offer library preparation services for some NGS applications such as mRNA-Seq, Exome-Seq. As part of our service, we will also check the quality of samples and advise you should the samples not meet the quality requirements. We are also in the process of optimising library preparation for more NGS applications and will update the website as we are ready to offer those as a service.

Methylation profiling

DNA methylation plays an important and dynamic role in regulating gene expression. Aberrant DNA methylation (hyper- or hypomethylation) and its impact on gene expression have been implicated in many disease processes, including cancer, neurological disorders, aging and development. (1,2)

The Illumina Infinium MethylationEPIC BeadChip allows profiling of over 850,000 methylation sites at single nucleotide resolution (> 90% of the original CpG sites from Human Methylation 450BeadChip plus an additional 350,000 CpG sites in enhancer regions). Multiple samples can be processed in parallel to provide a broad and comprehensive view of the methylome.

We facilitate research projects requiring methylation profiling by performing bisulfite conversion, quality control and liaising with the UCL Genomics Facility to get those samples processed on the Infinium MethylationEPIC BeadChips.

We also process FFPE samples for methylation studies by including extra QC and DNA restore steps to the standard protocol.

  1. Portela A, Esteller M. Epigenetic modifications and human disease. Nat Biotech. 2010;28:1057-1068
  2. Rakyan VK, Down TA, Balding DJ, Beck S. Epigenome-wide association studies for common human diseases. Nat Rev Genetics. 2011;12(8):529-541
Sequencing

Our Facility also provides sequencing services only if you wish to prepare your own libraries. We have access to MiSeq, NextSeq 550 and HiSeq 2500 instruments to cater for both small and large genomics projects. Based on your study requirements, we can advise on relevant sequencing kits and consumables that will be needed for your sequencing runs. 

Please contact CI.GAGE-facility@ucl.ac.uk to request the order form for submitting your samples.

Genome Engineering Services

 Please note that these services are available only to members of UCL

Open Biosystems pGIPZ lentiviral shRNAmir RNAi Libraries

We currently have the following shRNA libraries:

  • Open Biosystems pGIPZ lentiviral shRNAmir library- HUMAN
  • Open Biosystems pGIPZ lentiviral shRNAmir library- MOUSE

These libraries can be purchased as individual hairpins or as pooled libraries for multiplex screening.

You should contact your safety officer prior to beginning this work to ensure you have all the appropriate risk assessments and safety precautions in place. Sonia Buckingham is the Health and Safety Lead for the UCL Cancer Institute: s.buckingham@ucl.ac.uk

Open Biosystems pGIPZ shRNAmir library details

We have the Human and Mouse Open Biosystems GIPZ shRNAmir lentiviral libraries. Both libraries contain over 100,000 active clones, each containing a unique hairpin to target knockdown of genes within the Human and Mouse genomes respectively.

shRNAmir

The design of the hairpins contained within the GIPZ vector is based on the endogenous mir-30. By mimicking an endogenous RNA, the GIPZ hairpin is efficiently processed in vivo allowing for a more effective knockdown of your gene of interest.

Genomics and Genome Engineering mir30

GIPZ vector design

The GIPZ lenti-vector contains various features to allow effective expression, tracking and versatility of your hairpins. These features include:

  • CMV (Pol II) promoter
  • Turbo GFP to mark shRNAmir expression
  • Puromycin selectable marker
  • Lentiviral vector to allow successful transduction of primary, non-dividing and other difficult to transduce cells

pgipz…

Further information

pgipz standard…

Ordering

Individual hairpin clones

These GIPZ hairpins and any derivatives (viruses, cell lines, portions of the GIPZ vector cloned into other vectors etc.) must not be shared or transferred to institutes outside UCL. They must remain and be used solely within UCL laboratories.

You should contact your safety officer prior to beginning work with GIPZ hairpins to ensure you have all the appropriate risk assessments and safety precautions in place.

Formats

Individual hairpins come as bacterial agar stab cultures. You will need to re-streak the bacteria from the surface of the culture onto an LB-Amp plate, pick a single colony, grow, prepare and purify your plasmid DNA using a kit and sequence the DNA to make sure the sequence is correct. The DNA is then ready for transfection.

Controls

Negative:

  • Empty GIPZ vector
  • Non-silencing (scrambled) (22mer: aTCTCGCTTGGGCGAGAGTAAG)

Positive:

  • GAPDH (22mer: cCCTCATTTCCTGGTATGACAA)
  • EG5 (22mer: cGGCCATGCTAGAAGTACATAA) Targets Human but not Mouse

Controls are the same price as the shRNA hairpins and can be ordered by contacting CI.GAGE-facility@ucl.ac.uk to request the order form.

UCL Consortium prices

This includes members of the UCL Cancer Institute, Institute of Child Health, Institute of Neurology and the Division of Infection and Immunity.

Bacterial Stab Cultures: £15.00

Ordering clones

Instructions:

  • Contact CI.GAGE-facility@ucl.ac.uk to request the order form
  • Go to the GE website and follow the GIPZ Ordering Instructions to search for available hairpins. We have all of the Human and Mouse GIPZ hairpins within our collection starting with the codes V2LHS, V3LHS, V2LMM or V3LMM.
  • Take note of the CloneID for the hairpins you would like
  • If you are not from within the Cancer Institute, please make sure that you fill in your project details and Finance contact within your institute on the order form to enable us to generate an eIDT. Refer to the price list above, if you are unsure please contact us at CI.GAGE-facility@ucl.ac.uk
  • Complete the ordering form:
    • Make sure you enter your project code (CI as well as non CI users)
    • Indicate whether you would like any controls and what format you would like
    • List the the CloneID of the hairpins you are after. These codes will start with V2LHS, V3LHS, V2LMM or V3LMM
  • Email your completed form to CI.GAGE-facility@ucl.ac.uk. We will contact you to let you know your order has been received and to arrange collection. All clones are collected from the UCL Cancer Institute, Paul O'Gorman Building.

Sequencing your hairpins

We highly recommend sequencing your hairpins before starting work with them.

GIPZ sequencing primer: 5' - GCATTAAAGCAGCGTATC - 3' Melting Temp: 52.7c The binding site for this primer is base 5820-5842 and runs in reverse complement direction.

    CRISPR sequencing service

    Our Facility also runs a highly cost-effective targeted MiSeq CRISPR amplicon sequencing service to sequence edited cell populations or single cell clones. The CRISPR sequencing service was developed 'in house' to provide deep sequencing of amplicons derived from CRISPR-targeted genomic loci. The advantage of this method is the ability to identify and quantitate the type of insertions and deletions (indels) in any given sample, at the sequence level. Please contact us on CI.GAGE-facility@ucl.ac.uk for more information and associated costs.

    CRISPR Reagents

    We provide support in the design, production and use of the latest CRISPR technologies as well banking and distribution of associated in-house developed CRISPR reagents.

    Please contact CI.GAGE-facility@ucl.ac.uk for more information and protocols for the CRISPR reagents that we have, including CRISPR/Cas9 Plasmids.

    CRISPR/Cas9

    Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated systems 

    The CRISPR/Cas9 system is currently the most popular genome engineering technology available. It is a DNA binding complex based on a bacterial immune system that can be easily customised to target a specific sequence of DNA.

    CRISPR graphic…

    The system utilizes two components 1) a short guide RNA (gRNA) to recognise and bind target DNA and 2) a CRISPR associated (Cas9) endonuclease. When expressed together, the gRNA and Cas9 form an active endonuclease. The gRNA binds to the target sequence guiding a wildtype Cas9 to cleave the double stranded DNA in a site specific manner and resulting in DNA editing via DNA repair pathways.

    The CRISPR/Cas9 system is very versatile and many Cas9 variations exist. This includes nuclease deficient Cas9, which allows this system to be used as a DNA activation, repression, localization or purification tool and so on.

    The CRISPR/Cas9 system is a rapidly changing and advancing technology. New CRISPR/Cas9 reagents are constantly being developed, expanding even further upon the capabilities of this system. The CAGE facility aims to help researchers to utilise this system.

    We currently have a number of CRISPR/Cas9 reagents that can be ordered from the facility.

    Lentiviral Production

    We can provide high titre, second and third generation lentivirus directly from the Open Biosystems Human and Mouse whole genome shRNA libraries (for information on the libraries, please see the link above for RNAi Libraries). We also offer a custom lentiviral packaging service that is dependent on the provision of a suitable second or third generation lentiviral vector by the researcher. Please contact us on CI.GAGE-facility@ucl.ac.uk for more information and associated costs.