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Blizard Institute - Faculty of Medicine and Dentistry

Genome Centre

Barts and The London Genome Centre is the genomics core facility at Queen Mary University of London, supporting researchers since 2000.

We work with academic (both with and without Queen Mary affiliation) and corporate partners on a not for profit basis to achieve their genomics research aims. Ours is a highly collaborative model, providing a custom service, offering advice on design and interpretation as required.
We are always interested in trying novel approaches to genomic challenges.

All Genome Centre services are booked through iLab - What is iLab?

Talk to the Centre Manager

Book services and equipment

Single Cell Genomics

Single cell genomics is used to unpack cell heterogeneity, often within a tissue or cancer biology.  We have been running chemistry from 10X genomics since 2018. A modular approach means whole transcriptome information can be augmented with a combination of T and B cell receptor profiling, surface bound protein, and chromatin accessibility.

Talk to the team about single cell genomics

Application Protocol Species Description
Transcriptomics 3' tag Sequencing Any Poly A priming used to generate a 100bp tag from the 3' end of each cell's transcript
Transcriptomics 5' tag Sequencing Any Poly A priming used to generate a 100bp tag from the 5' end of each cell's transcript
Epigenetics (Chromatin accessibility) Assay for Transposase-Accessible Chromatin (ATACseq)

Any

Open chromatin is accessible to tranposase enzyme generating cell specific libraries only in these regions
Transcriptomics and Epigenetics (Chromatin accessibility) Multiome Any ATACseq and 3' libraries generated from each cell
Immunobiology T Cell Receptor Profiling Human or Mouse PCR primers used to amplify the VDJ region from cDNA generated by the 5' protocol
Immunobiology B Cell Receptor Profiling Human or Mouse PCR primers used to amplify the VDJ region from cDNA generated by the 5' protocol
Proteomics Surface Marker Profiling (CITESeq, feature barcoding) Any DNA barcoded antibodies used to measure protein level.  Compatible with either 5' or 3' transcriptome libraries

 

Spatial Biology

Using Spatial biology technologies it is possible to analyse RNA and Protein  whilst retaining their two dimension position information in the original tissues. We can offer solutions from both 10X Genomics (Visium Chemistry), for which we are the only certified supplier in the South of England, and Nanostring (GeoMX DSP).

Talk to the team about spatial biology

Technology Tissue Type Species Analyte Chemistry Feature Size & Number

Visium 10X Genomics.
Mouse Embryo E17.5 profiled with 11mm X 11mm Visium slide (14,336 spots)

Fresh frozen

Any Species

RNA (full transcriptome)

PolyA primed 3' tagged sequencing

50 micron

4992
FFPE Human or Mouse  RNA (~18,000 human genes, ~19,500 mouse genes) Probe based sequencing

 50 micron

4992 or 14336

GeoMX Nanostring
Tumour section with two regions of interest

Fresh frozen

Human or mouse

RNA (~18,000 human genes, ~ 21,000 mouse genes)

Probe based sequencing 

 

100 to 600micron

up to 192

FFPE Human or Mouse  RNA (~18,000 targets) Probe based sequencing 

100 to 600 micron

up to 192

Fresh frozen Human or Mouse Protein (panels of 10) Nucleotide tagged antibody sequencing

100 to 600 micron

up to 192

FFPE Human or Mouse Protein (panels of 10) Nucleotide tagged antibody sequencing

100 to 600 micron

up to 192

 

RNA Analysis

We run a range of different platforms and implement or develop methods that cover all scales of genomic questions.

 

Talk to the team about RNA profiling

Technology Assay

 

MiSeq

Next Generation Sequencing - Illumina NovaSeq, NextSeq, and MiSeq

Whole Transcriptome Analysis, options to profile protein coding RNA, total RNA and miRNA from bulk samples.  See our guide to RNA seq
 

Real-time PCR

- ABI QuantStudio 7 Flex Real-Time PCR System 

qPCR (real time PCR) is still the gold standard to analyze individual RNA. Learn more about our qPCR service  

 

DNA Analysis

We run a range of different platforms and implement or develop methods that cover all scales of genomic questions.

Talk to the team about spatial DNA analysis

Technology Assay

 

MiSeq

Next Generation Sequencing - Illumina NextSeq and MiSeq

Whole Genome Sequencing (WGS)
Whole Exome Sequencing (WES) using  Agilent Sure Select or similar
Targeted Region Sequencing with either Fluidigm Access Array or Agilent Sure Select
Metagenomics with either 16s DNA or whole genome sequencing
 

Arrays 

- Illumina Bead Arrays 

To run genome wide association studies (GWS) Genome Wide or Custom SNP arrays
 

Real-time PCR

- ABI QuantStudio 7 Flex Real-Time PCR System 

Genotyping individual single nucleotide polymorphisms (SNP) in large cohorts we use SNP genotyping Taqman

Sanger Sequencing

- ABI 3730

Sequencing individual plasmids or PCR products see our Sanger Sequencing guide
An example of a microsatellite

Microsatellite (Short Tandem Repeat (STR)) Genotyping

- ABI - 3730

Off the shelf panels can be used for human identification and cell line validation.  Custom panels are often used to study population genetics

 

Epigenome Analysis

Understanding the control of gene expression through DNA methylation and chromatin accessibility is key to decoding cell circuits.  We offer a range of scales to study DNA methylation of which the most cost effective approach is using Infinium arrays form Illumina  targeting hundreds of thousands of GpG sites.

Talk to the team about epigenomics

Technology Assay

 

MiSeq

Next Generation Sequencing - Illumina NextSeq and MiSeq

DNA Methylation Analysis

Whole Genome Bisulphite Sequencing  

DNA Methylation Analysis

(WGBS)Reduced Representation Bisuplhite Sequencing

DNA Methylation Analysis

(RRBS)Targeted Bisulphite

DNA Methylation Analysis

Targeted Region Sequencing with Fluidigm Access Array or individually

 

Arrays 

- Illumina Bead Arrays 

DNA Methylation Analysis

Infinium EPIC Arrays (human 850,000 CpG sites)

Infinium mouse methylation arrays (mouse 265,000 CpG sites)

 

Next Generation Sequencing - Illumina NextSeq and MiSeq

Chromatin Accessibility

Assay for Transposase-Accessible Chromatin (ATACseq).

 

Bioinformatics

Genetics and genomics studies produce ever larger data sets.  Having a strategy to analyse the results of a project is all important. 

The Centre can help with a guided analysis for RNAseq, Single Cell Sequencing, and Spatial Genomics using a commercial solution from Partek (Partek Flow) for which QMUL has a cloud based instance.  We run a preliminary analysis and provide a user login to view and interrogate the results. Partek Flow requires no prior coding experience and uses a point and click based interface making it a great solution for many users.

For more bespoke applications we have bioinfomatics support to answer novel questions and to develop new tools. We take advantage of the QMUL High Performance Cluster (Apocrita) and run computationally intense processes in order to analyse data that cannot be analysed on a standalone desktop. We have experience in Bash, R and Python programming languages and associated packages, and have worked on bespoke analyses for Flow Cytometry, DNA sequencing (variant calling), single cell and spatial transcriptomics and metagenomics to name a few. We are open to and love to analyse new data types in order to answer specific biological questions.

Talk to the team about bioinformatics

Commonly used workflows in Partek
Application Partek web tutorial Our workflow Examples

RNA Sequencing

RNAseq analysis with Partek Flow

Seq QC, alignment, PCA, differential gene expression, pathway analysis

 

Single Cell Genomics

Single-cell-RNAseq with Partek-Flow

Initial processing with Cell Ranger (10X Genomics), Seq QC, PCA, UMAP, clustering, differential gene expression, pathway analysis  

Spatial Transcriptomics

Spatially resolved 'omics data with Partek

Initial processing with Space Ranger (10X Genomics), Seq QC, PCA, UMAP, clustering, spatial overlay, differential gene expression, and pathway analysis  

 

We have a dedicated team of very experienced scientists

 

Charles Mein

 Eva Wozniak

 

Professor Patricia Munroe, Director

Patricia became Director of the Bart's and The London Genome Centre in 2016, taking over from David vanHeel. Patricia is internationally renowned geneticist with research interests in cardiovascular and blood pressure phenotypes.

Publications

 

Dr Charles Mein, Manager

Charles studied Genetics at undergraduate level before working on the Genetics of Type 1 Diabetes for his Dphil. He was recruited in 2000 to establish the Centre which focused on the genetics of complex disease. Under his leadership the Centre has kept pace with the rapid technological changes in the genomics field.

Publications

 

Eva Wozniak, Deputy Manager

Eva joined our team in 2011 after working on research into women’s cancers at the Institute for Women’s Health at UCL for 6 years.  Her areas of expertise are many, covering all of the activities we specialise in. She has established many services at our Centre, including Spatial Genomics, Single Cell genomics, and RNA seq.

Publications

 Paul Stevens

 Salina Thapa

 Bryna McCarthy

 

Paul Stevens, Technician

Paul is currently working on single cell genomics and spatial biology.  He joined us in spring 2021 having worked previously at UCL for many years running their Sanger sequencing service.

Publications

 

Salina Thapa, Technician

Salina is a new member of our team, starting in Jun 2022, having recently gained her MSc Medical Microbiology followed by service in one of the COVID testing centres.  She will be joining the single cell genomics part of our team.

Publications

 

Bryna McCarthy

Bryna started with us at the end of June 2022, having previously worked with the BGI in their COVID testing facility.  She has an MSc in  "Cancer, Molecular Pathology and Genomics" from Barts Cancer Insitute.

 James Boot

 

Laura Caton, Technician

Laura joined us in September 2022.  She's a recent graduate from the UCL MSc in Genetics of Human Disease for which she best in her class.  She joined us with experience in Nanopore sequencing.

 

 Dr James Boot, Bioinformatician

James joined our team in spring 2021 following a PhD here at the Blizard Institute with Prof Silvia Marino. He's set up analysis workflows for single cell, spatial, RNAseq, flow cytometry, metagenomics, DNA variant calling and more! James has worked collaboratively with many researchers in this area and loves an analysis challenge.

Publications

 

 

 

The Genome Centre is located in purpose built lab space in the RIBA award winning Blizard Institute on Queen Mary’s Whitechapel Campus – building number 6 in the campus map, just a short walk from Whitechapel Underground Station.
Blizard Building at night
Our postal address is:

Genome Centre 
Barts and The London 
School of Medicine and Dentistry 
Blizard Institute 
4 Newark St
Whitechapel
London 
E1 2AT

Tel +44 207 882 2055 (Manager)
Tel +44 207 882 2058 (Lab Staff)

Or find us on Google Maps - search "Genome Centre"

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