Unlock the hidden signal with single-cell analysis

Single-cell resources

The Oxford Genomics Centre as part of the Wellcome Centre for Human Genetics is a partner in the Oxford Consortium for Single-Cell Biology (Oxford ConSiCe Biology), receiving a share in a £4.9M award from the MRC’s Clinical Research Capabilities and Technologies Initiative which has been used to develop single-cell capabilities
(see news item: Developing Single-Cell Capability).

We offer a wide and growing range of genomics applications for single cells, including RNA-seq, gene expression profiling, immune clonotype profiling, cell surface proteins, antigen specificity and chromatin accessibility. Applications are supported by the 10X Genomics Chromium platform, or in conventional multi-well plates using FACS (cell sorting) combined with low-volume, automated liquid handling.


The 10X Genomics Chromium™ Controller is a platform designed to deliver highly parallel sample partitioning and molecular barcoding. The broad portfolio of Chromium Single Cell solutions can capture molecular information of cell activity in multiple dimensions, including gene expression, cell surface proteins, immune clonotype, antigen specificity and chromatin accessibility.

The key to this technology is the ability to generate tens of thousands of single cell partitions, each containing an identifying barcode for downstream analysis. The instrument uses advanced microfluidics to perform single cell partioning and barcoding in a matter of minutes.

  • 10X Single Cell System features:
  • Complete workflow from cell suspension through sequencing-ready cDNA library
  • Extremely high-throughput allowing to capture 100 – 10,000 cells per sample
  • Robust performance, high cell capture efficiency
  • Compatible with Illumina® sequencers
  • A complete analysis and visualization package
  • Run 1 to 8 channels in parallel
  • No lower size limit on cells
  • Recover 30-65% of all loaded cells

Applications Supported by Oxford Genomics Centre:

The Chromium Single Cell 3’ Solution provides high-throughput, single cell expression measurements that enable discovery of gene expression dynamics and molecular profiling of individual cell types. Cell surface protein information can be added with the use of Totalseq Antibodies.

The Chromium Single Cell V(D)J Solution enables profiling of full-length paired V(D)J transcripts from thousands of lymphocytes.  This solution allows assembly of full-length V(D)J sequences on a cell-by-cell basis, providing high-resolution insights into the adaptive immune system. Gene expression can be combined with immunophenotyping using the Totalseq Antibodies to better describe immune cell subsets and functional states.

The Assay for Transposase Accessible Chromatin (ATAC) for epigenomic analysis of thousands of individual nuclei provides insight into cell types and cell states for deeper understanding of gene regulatory mechanisms.

Designed to simultaneously profile gene expression and open chromatin from the same cell allowing characterisation of cell types and states, and uncover gene regulatory programs.

A defined set of transcripts from single cells or tissue sections can be profiled with Targeted Gene Expression. Customizable, comprehensive gene panels will allow reduced sequencing costs of your samples.

Available panels include Human Pan-Cancer Panel, Human Immunology Panel, Human Gene Signature Panel and the Human Neuroscience Panel. It is also possible to design custom panels and further information can be found on the 10X site.

This technology allows mapping of the whole transcriptome with morphological context of the tissue. Oxford Genomic Centre can support library preparation and sequencing of cDNA samples derived from Visium solution.

• Antibodies for cell surface protein analysis can be added for an extra layer of information. This solution is compatible with 3 prime and V(D)J Solutions. Individual antibodies or pre-designed panels are available from Biolegend.
• 10X’s CellPlex solution for cell hashing and multiplexing uses a series of oligonucleotides conjugated to a lipid, allowing for subsequent pooling of multiple samples to be run on single channel. Benefits of hashing include a reduction of doublet rate, minimising of batch effects and a cost reduction of complex experiment
• Peptide-MHC multimers to measure antigen specificity. Assess the specificity of the adaptive immune system at single cell resolution with simultaneous capture of paired T cell receptors and peptide-MHC multimers, or immunoglobulin heavy and light chains and their cognate antigens.


For more information please visit: www.10xgenomics.com.
To discuss your project requirements please contact us.

SH800Z cell sorter features a novel microfluidics sorting chip integrated with comprehensive fluidics controls to simplify system and sort setup.

A flexible optical design offers up to 4 collinear excitation lasers (488 nm, 405nm, 561nm and 638nm) and 6 fluorescence detectors. The six free-form PMTs enable detection of fluorescence signals from any laser based on filter selection.


  • Sorting into tubes and a range of multi-well plates (96- and 384- well plates) is fully supported
  • Novel microfluidics sorting chip and comprehensive fluidics controls to simplify sorting
  • Exchangeable sample fluidics
  • 4 collinear excitation lasers (488 nm, 405nm, 561nm and 638nm) and 6 fluorescence detectors
  • Index sorting analysis capability in the software records the X and Y co-ordinates of each event sorted in a multi well device. Using this feature, end-users can reference the scatter and fluorescence data of the sorted events as well as determine the location of a sorted event in a multi-well plate
  • The SH800 interrogates cells in samples using up to four lasers (405 nm, 488 nm, 561 nm, 638 nm). It measures forward scatter, back scatter, and six channels of fluorescent light

OGC offers a complete workflow from cell suspension to sequencing-ready library.

Please contact us if you’re interested in using our cell sorting facility.

Before you begin

It can take some time to decide on your preferred experimental design through discussions with our team. Once this is finalised, you should request a quote from our project management team at least 2 weeks before you wish to go ahead with a run.

In order to proceed with your run, a submission form must be received by your project manager 48 working hours in advance. If the submission form is not received, the run WILL BE CANCELLED.

Our sample guidelines contain more information about the steps required in advance of a run and sample requirements.