Wellcome Sanger Institute
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Single Cell Genomics Core Facility

Scientific Operations

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Scientists hope to gather a new understanding of biology by closely examining the fundamental units of life - single cells. Recent technological improvements have now enabled scientists to sequence the genome and the epigenome, i.e. the programming, as well as the transcriptome, i.e. the "current" programming, of single cells. These methods allow us to get a better understanding of cell types, how different cell types interact and change throughout their life. This research has implications in general cell biology, cancer, immunology and infectious diseases.

In our core facility, we employ integrated microfluidic systems like the Fluidigm C1, acoustic dispensing, conventional flow sorting of single cells and liquid handling robots to deliver thousands of single cell genomes, transcriptomes and epigenomes per day, complemented by a fully automated sample handling, QC and library preparation pipeline.

In the beginning of every single cell experiment stands the challenge to dissociate tissues and isolate single cells into reaction containers. We support our scientists by gathering knowledge across teams on how to best isolate specific cell types from various tissues and by making this knowledge widely available. We employ microfluidic cell isolation procedures, e.g. by Fluidigm, and custom procedures that utilise microdroplet fluidics, very specific cell isolation using precision micromanipulation and laser capture microdissection, as well as high-throughput index sorting in our Cytometry Core Facility into 384w microwell plates.

After isolation, cell can be subjected to a range of protocols depending on the scientists requirements. For single cell RNAseq and whole genome amplification, we offer either the Fluidigm C1 platform as a user operated instrument or an automated high-throughput pipeline based on liquid dispensers. For more sophisticated protocols like &GTseq or scBisulphite Seq, we use conventional tip-based liquid handling systems that are integrated with a number of other components to offer a walkaway solution.

After amplification, all cell samples are subjected to a cleanup procedure and sample QC procedure that utilises tip-based liquid handlers and a novel type of acoustic dispenser. This particular instrument allows us to assess sample quality by transferring only 100 nl of a sample into specific assays. After quality control, libraries are set up on the same acoustic dispenser. Our current procedure uses up to 500 pg of cDNA/DNA to generate libraries in a volume of less than 1 µl. This unique technology helps us to significantly reduce cost while delivering a throughput of thousands of cells per day. This technology is not limited to library preparation, but can also be utilised for high-throughput qPCR and method development. All libraries are then quality controlled and submitted for sequencing by our in-house sequencing teams.

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                            [post_excerpt] => Matt works within the DNA Pipelines Research and Development group where he helps to develop and implement novel protocols used by&nbsp;<span title="... the operational sequencing teams. Matt&rsquo;s skills and experience range from NGS library preparation and automation to troubleshooting sequencing quality issues.">...</span>
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    [excerpt] => Our aim is to offer a high-quality, high-throughput single cell sequencing service that enables Faculty to study and understand cellular heterogeneity and it’s role in health and disease. We further want to create a collaborative and open environment to foster single cell method development.
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                            [post_excerpt] => We use cutting edge single cell genomics technologies and computational methods to understand genes, proteins and cells in human health and&nbsp;<span title="... disease. We have a long-standing interest in understanding global principles of gene regulation, protein interactions and have a particular interest in immunity.">...</span>
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                            [post_excerpt] => John Marioni's group develop computational and statistical tools to exploit high-throughput genomics data to understand the regulation of gene expression&nbsp;<span title="... and to model developmental and evolutionary processes. His team has pioneered approaches for analysing single-cell transcriptomics data and, together with four colleagues, he co-ordinates the Sanger Institute-EBI Single-Cell Genomics Centre.">...</span>
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    [introduction] => Scientists hope to gather a new understanding of biology by closely examining the fundamental units of life - single cells. Recent technological improvements have now enabled scientists to sequence the genome and the epigenome, i.e. the programming, as well as the transcriptome, i.e. the "current" programming, of single cells. These methods allow us to get a better understanding of cell types, how different cell types interact and change throughout their life. This research has implications in general cell biology, cancer, immunology and infectious diseases.
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    [partners_introduction] => We work closely with the groups below, both delivering a service to them and getting their input and assistance in developing and improving methods.
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                            [post_title] => Sanger Institute-EBI Single-Cell Genomics Centre
                            [post_excerpt] => We are developing and applying methods to explore the genome, epigenome and transcriptome of single cells in order to better understand&nbsp;<span title="... normal development and disease processes.">...</span>
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    [title] => Single Cell Genomics Core Facility
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                    [content] => <p>In our core facility, we employ integrated microfluidic systems like the Fluidigm C1, acoustic dispensing, conventional flow sorting of single cells and liquid handling robots to deliver thousands of single cell genomes, transcriptomes and epigenomes per day, complemented by a fully automated sample handling, QC and library preparation pipeline.</p>
<p>In the beginning of every single cell experiment stands the challenge to dissociate tissues and isolate single cells into reaction containers. We support our scientists by gathering knowledge across teams on how to best isolate specific cell types from various tissues and by making this knowledge widely available. We employ microfluidic cell isolation procedures, e.g. by Fluidigm, and custom procedures that utilise microdroplet fluidics, very specific cell isolation using precision micromanipulation and laser capture microdissection, as well as high-throughput index sorting in our <a href="https://www.sanger.ac.uk/group/cytometry-core-facility/">Cytometry Core Facility</a> into 384w microwell plates.</p>
<p>After isolation, cell can be subjected to a range of protocols depending on the scientists requirements. For single cell RNAseq and whole genome amplification, we offer either the Fluidigm C1 platform as a user operated instrument or an automated high-throughput pipeline based on liquid dispensers. For more sophisticated protocols like &amp;GTseq or <a href="https://www.sanger.ac.uk/group/reik-group/">scBisulphite Seq</a>, we use conventional tip-based liquid handling systems that are integrated with a number of other components to offer a walkaway solution.</p>
<p>After amplification, all cell samples are subjected to a cleanup procedure and sample QC procedure that utilises tip-based liquid handlers and a novel type of acoustic dispenser. This particular instrument allows us to assess sample quality by transferring only 100 nl of a sample into specific assays. After quality control, libraries are set up on the same acoustic dispenser. Our current procedure uses up to 500 pg of cDNA/DNA to generate libraries in a volume of less than 1 µl. This unique technology helps us to significantly reduce cost while delivering a throughput of thousands of cells per day. This technology is not limited to library preparation, but can also be utilised for high-throughput qPCR and method development. All libraries are then quality controlled and submitted for sequencing by our in-house sequencing teams.</p>
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    [created_at] => 2015-10-15 11:14:03
    [updated_at] => 2020-08-13 13:52:34
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Core team

Photo of Matthew Mayho, PhD

Matthew Mayho, PhD

Staff Scientist