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  3. Genomics
  1. Home
  2. Core Facilities
  3. Genomics

State-of-the-art DNA and RNA analysis instruments, methods and applications, in particular next-generation sequencing and cutting-edge single-cell and spatial single-cell technologies to facilitate research.

The Genomics Core provides sequencing on the latest Illumina next-generation sequencing and ONT long read technologies. These allow 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 also provide library preparation services (LPS); typically for genomes, exomes, transcriptomes, and ChIP-seq experiments. We have a standard list of LPS on offer, please discuss your LPS needs with us prior to any submissions. If you have a project in mind, get in touch and we advise on the best approach for your samples, depending on the quality of nucleic acids, scope of your project, and available budget. 

The cutting-edge disaggregated single cell library preparation and spatial single cell methods are our passion. We have variety of single cell workflows mainly based on 10X Genomics technology but also many others including plate-based methods using a low volume liquid handling robot. Again, if you have project in mind, just talk to us. 

We are also able to offer a full service for sequencing, and library prep, where we perform the steps from sample-to-data. In addition, we house equipment for self-service use, where you have access to training, equipment, reagents and consumables, but do the work yourself. 

Dr Ania Piskorz

Head of Genomics

Genomics help

For more details including how to submit your sample or discuss your project with us, please visit: Genomics Help 

If you have any questions about the sequencing or bulk DNA/RNA library preparation or any other general requests or would like to discuss your project with us before you start, please e-mail us: genomics-helpdesk@cruk.cam.ac.uk 

For any questions related to single cell projects/technologies discuss your project with us before you start, please e-mails us: singlecell@cruk.cam.ac.uk 

Focus areas

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NGS and long read sequencing

Our sequencing service is available across the University of Cambridge, originally born from a collaboration with several partners and departments coordinating efforts to develop the infrastructure. 

Run types by sequencer:

MiSeq runs allow a maximum number of cycles depending on the reagent cartridge, but you can request any length and single- or paired-end as required as you own the whole flowcell.

Most of our sequencing is carried out on Illumina’s NovaSeqX Plus, NovaSeq6000 but also NextSeq2000 and we can still perform almost any run configuration, including custom primers for your specific libraries. The most commonly requested runs remain paired-end (PE)150 bp and paired-end (PE)50 bp, but as more and more single cell or CRISPR screen experiments are sequenced we see interesting trends to asymmetric PE reads to incorporate UMI’s and more creative barcoding strategies. So, if in doubt just ask. Even for a single lane request with interesting parameters we can often find a suitable partner to enable a flowcell to be run. 

We now also offer long read sequencing using ONT (Oxford Nanopore Technologies) PromethION24, so if you are interested in this technology or would like to read out modified bases without manipulating DNA or RNA templates, get in touch.  

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Library preparation for bulk DNA & RNA

We have several different library preparations for bulk DNA and RNA: 

  • Amplicons, small genomes, plasmids: Illumina, NexteraXT 
  • Long read ONT LPS: ONT ligation, ONT rapid ligation, ONT Direct RNA, ONT cDNA-PCR, ONT PCR-cDNA and ONT single cell 10X cDNA 

We tune all workflows depending on the quality of your material and aims of the project. If you would like to discuss your project with us, just get in touch, we will advise on the best approach. We have a lot of expertise in working with challenging material like low nucleic acid input or poor quality like FFPE samples. 

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Single cell omics

We have two main single-cell library construction strategies: 

  • Variety of workflows mainly based on 10X Genomics but not only: 3′ mRNA-seq for gene expression, 5′ gene expression, V(D)J targeted for immunological studies, ATAC-seq, CITE-seq and Mutiome (3′ mRNA-seq and ATAC-seq on the same nuclei) 

 

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Spatial single cell omics

Among the spatial platforms to map transcriptome within the tissue context we have expertise in:  

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Additional equipment

Our core also uses: 

  • Agilent 2100 Bioanalyzer for automated DNA and RNA electrophoresis and protein analysis 
  • Cellenion CellenOne for single cell isolation 
  • Covaris S220 ultrasonicator for DNA, RNA or chromatin shearing, tissue homogenization or cell lysis 
  • Covaris LE220 high-throughput ultrasonicator for DNA, RNA or chromatin shearing, tissue homogenization or cell lysis, for 1 – 96 samples 
  • Standard Biotools (Fluidigm) Juno for hi-plex PCR or amplicon library preparation, as well as RNA-seq (GEX) library prep. 
  • Standard Biotools (Fluidigm) Biomark HD: high-throughput microfluidic system for single-cell gene expression analysis, digital PCR, and amplicon-based target enrichment 
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Liquid handlers

  • SPT Labtech Mosquito HV liquid handler for dispensing reagents 
  • Formulatrix Mantis for dispensing reagents 
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NGS method and applications

Uses of NGS: The most common applications today are sequencing of whole genomes, exomes, amplicons, transcriptomes (commonly referred to a ‘RNA-seq’, but be careful, there are very many different ‘RNA-seq’ methods depending on the RNA species you are looking for…) and DNA:protein interactions (ChIP-seq). NGS sequence reads can be generated as either single-end, where only one end of a fragment molecule is sequenced or as paired-end, where both ends are sequenced. These days we mainly run PE (same cost as SE) but you could use only one read for your analysis. The format of a sequencing run is generally chosen before library preparation and there are a few commonly accepted defaults, e.g. PE-50bp mRNA or PE-150 for cancer genomes or 28:90 for 10X 3’ etc. The structure of a sequencing data set is determined by the question being asked. ChIP-seq studies require high numbers of short-reads so these are generated on short fast runs. WGS requires as much actual genome coverage as possible so longer-reads are used. RNA-seq and Structural-Variation-seq can use varying lengths of sequence read but both use paired-end data for many studies. 

Whole genome sequencing: Tens of thousands of Human genomes have now been sequenced, with the majority of these completed on the Illumina platform. The costs of a genome sequencing is rapidly decreasing and is now $200. 

  • 30-50x genome coverage using long paired-end reads, generally 450M PE-150 reads per sample 

Exome-seq or Capture-seq: It is possible to sequence just the exons or targets of your interest which reduces the time and cost of experiments and allows a significant increase in sample numbers. Data analysis is potentially easier as well. Most exome sequencing is performed using in-solution capture. In this method biotinylated-oligonucleotide baits are mixed with sequencing libraries to pull-down only the exon regions for sequencing. 

  • 50x exome coverage using PE-150 paired-end reads, generally 30-50M PE-150 reads per sample 

Amplicon-seq: For many research questions simply sequencing one or two exons in hundreds of samples is faster, uses little DNA for analysis and data analysis is simple. PCR amplification is well understood and has high specificity and sensitivity. Most users can simply design their own assays and it is theoretically possible to generate sequence data in one week, from primer design and ordering, PCR and sequencing. As potentially 100’s of samples can be multiplexed into a single NGS run the cost per sample or per amplicon can be very low, less than $1 each. 

  • 50-2000x amplicon coverage using long paired-end reads, generally 1-5M PE-150bp reads per sample 

ChIP-seq: The analysis of Protein:DNA interactions allows researchers to unravel genome regulation and it’s influence on gene expression and methylation. Their most common application is the analysis of transcription factor binding: native DNA is cross-linked to bound proteins and fragmented; fragments bound to proteins are enriched by immunoprecipitation with an anti-body to the protein of interest; this DNA is then used in a library preparation ready for NGS sequencing. CLIP-Seq is a very similar method used for Protein:RNA interaction analysis. 

  • Generally 10-50M PE-50 reads per sample, more, > 2 replicates 

  RNA-seq: Actually several very different methods are commonly referred to as RNA-seq: differential gene expression by mRNA-seq with a small number of reads (10-20M PE-50), small RNA-seq with even fewer reads (1-2M PE-50) and whole transcriptome analysis from mRNA enriched or ribosomal RNA-depleted total RNA for the analysis of all RNAs, splicing and allele specific expression. Most start with RNA that is converted to cDNA for library preparation and finally sequencing. These are among the most popular applications we run on our Illumina sequencers. 

  • DGE: Generally 20M PE-50 reads per sample 

Group Members

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    Ania Piskorz

    Head of Genomics

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    Johanna Barbieri

    Principal Scientific Associate

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    Jason Skelton

    Senior Scientific Associate

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    Alex Deamer

    Research Assistant

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    Ugurcan Sal

    Research Assistant

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    Rachel Barnes

    Research Assistant

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    Marina Golotiuk

    Research Assistant

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    Maribel Valenzuela

    Research Assistant

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    Eleanor Denham

    Research Assistant