Unlock the hidden signal with single-cell analysis

Single-cell resources

The Oxford Genomics Centre as part of the Wellcome Trust 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 will be 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 by qPCR and DNA amplification for whole-genome or targeted (exome or PCR-based analysis). Applications are supported by the Fluidigm C1 Single-Cell Auto Prep and Polaris integrated research systems, 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. It supports a variety of applications, including the well-established 10X Genomics Linked-Read technology for genome analysis and the existing Chromium™ Single Cell 3’ Solution for single cell transcriptomics, allowing cell characterization and gene expression profiling of hundreds to millions of cells.

  • 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
  • Single Cell 3’ Solution for whole-transcriptome RNA-Seq
  • Single Cell V(D)J Solution for immunoprofiling
  • Recover 30-65% of all loaded cells
  • Load 100-10,000 cells


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.
The Chromium Single Cell V(D)J Solution is a comprehensive, scalable tool for profiling full-length paired V(D)J transcripts from hundreds to millions of lymphocytes. The new solution enables assembly of full-length V(D)J sequences on a cell-by-cell basis, providing high resolution insights into the adaptive immune system.
The Chromium Genome Solution provides long range information on a genome-wide scale, including variant calling, phasing and extensive characterization of genomic structure. Unlock critical genetic information for variants in heritable disorders, and discover key genomic alterations in cancer. Genomic data can be aligned to a well-defined reference, or assembled de novo to provide new assemblies in one step (see here).
The Chromium Exome Solution uses the power of linked-reads to fully resolve genic phasing, structural variation, and detect variants in previously inaccessible and complex regions of the exome, at lower cost than the Genome Solution.


For more information please visit: www.10xgenomics.com.
To discuss your project requirements please use our enquiry form or email us.

The C1 cell preparation system can isolate up to 96 cells and then process them to produce pre-amplified cDNA or amplified genomic DNA for downstream analysis, including sequencing on the Illumina platforms. The most commonly-used application is currently RNA-seq. The whole process from cell capture to sequence-ready libraries can now be automated to quickly and efficiently deliver gene expression data from many diverse cell populations.


This new, simplified workflow uses Fluidigm’s C1 Single-Cell Auto Prep System, Clontech’s SMARTer Ultra Low RNA input Kit for cDNA synthesis and Illumina’s Nextera XT Sample Preparation Kit for library preparation.


We have automated the downstream processing of C1 chips, from cDNA QC to the consolidation of samples from multiple chips to standard 96-well format plates, followed by library construction, pooling and QC. Cells can be selected for further analysis including sequencing, based on imaging data.

The new integrated Polaris system can be used to select, isolate, dose, culture and process individual cells ready for downstream molecular preparation and analysis. By coordinating cell selection, control of the cell’s biological conditions and immediate analysis of the cell’s genomic response, this system offers the ability to accurately correlate genotype and phenotype.


We also support read-out using the Fluidigm BioMark HD real-time PCR instrument and assay types that include Fluidigm and TaqMan custom assays in addition to RNA-seq.

We offer a range of service entry-points, from submitted cell samples to harvested C1 products and pre-made libraries. We also offer equivalent protocols undertaken on isolated cells, lysed cells and amplified materials in micro-well plates.

If you are interested in this technology please contact us for more details.


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 (SmartSeq2 combined with NexteraXT)

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.

More information about the steps required in advance of a run and sample requirements can be found in our submission guidelines here.