Technology Platforms and Training

The single cell technology platforms available through the OSCBC are housed in two facilities based at the WIMM and WTCHG providing access to state of the art technology platforms for research groups across the Oxford Campus. These facilities also provide carefully managed and “ultra clean” laboratory space required for single-cell genomics experiments.

Training

Platform specific training can be provided by the facilities for researchers wishing to independently conduct single-cell experiments including RNAseq, Fluidigm BioMark platforms and the nanoString platform.

Targeted Gene Expression Analysis

Both the WTCHG and WIMM facilities house Fluidigm BioMark platforms for high throughput single-cell or low cell number QPCR analysis. The WIMM facility also houses a nanoString platform which can be used for targeted gene expression analysis of single cells.

Microfluidic Cell Capture

Both the WTCHG and WIMM facilities house Fluidigm C1 systems for in-chip microfluidic cell capture and downstream workflows for mRNA-sequencing, DNA-sequencing, epigenetics (ATAC-seq) or MiRNA expression.

The WTCHG facility also houses a Fluidigm Polaris System which 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.

RNA-sequencing

Both the WTCHG and WIMM facilities have established workflows for RNA-sequencing of FACS isolated single-cells. Standard protocols are available for each stage in the workflow from cell lysis and reverse transcription through to cDNA generation, quality control and indexing of libraries.

Whole Genome Sequencing

Both the WTCHG and WIMM facilities have established workflows for whole genome amplification of FACS isolated single-cells.

Automated Liquid Handling

Both facilities house a number of platforms for precise and repeatable nanolitre liquid handling inclusing the Mosquito (WIMM), Labcyte Echo (WTCHG) and Beckman robotic liquid handling platforms (WIMM and WTCHG).

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Imaging

The Wolfson Imaging Centre – Oxford was established in 2012 with funds received from the Wolfson Foundation. The facility contains a number of platforms suitable for single-cell imaging.

Sequencing

Next generation sequencing platforms are available at the WIMM (MiSeq and NextSeq500) and WTCHG facilities (HiSeq 2500, HiSeq 4000 and MiSeq).

Mass Cytometry

The WIMM facility houses a Helios system for single-cell analysis of up to 40 proteins per cell using metal isotopes. Mass cytometry uniquely combines time-of-flight mass spectrometry with Maxpar metal-labeling technology to enable breakthrough discovery and comprehensive functional profiling applications. Cellular targets are labeled with metal-tagged antibodies and detected and quantified by time-of-flight mass spectrometry. The high purity and choice of metal isotopes provide minimal background noise from signal overlap or endogenous cellular components. And 135 available detection channels ensure an ongoing ability to add more parameters, enabling you to fully study the functional complexity of biological systems at the single-cell level.

Flow Cytometry

The WIMM has a large and developing flow cytometry facility catering for over 300 scientists. The facility has five sorters and seven analysers. Facility staff provide expert training, analysis and sorting services with specific expertise in the isolation of single-cells by FACS for downstream workflows. Both the WIMM and WTCHG also have the Sony SH800 FACS/Analysis. The SH800 provides the highest level of automation and ease of use available in a cell sorter. Researchers can accurately set-up, calibrate and monitor sorting with a push of a button, thus alowing non-specialist users to use the system without the need for a dedicated FACS technician.       

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Data Analysis

The OSCBC provided funding to establish a new purpose built Centre for Computational Biology due to open in June 2016. The Centre will include up to 40 computational scientists with expertise in bioinformatics, statistical genetics, imaging and analysis of data from single cells. The Centre will also provide the necessary infrastructure (storage and server capacity) through a centralized computational resource that will support all single cell genomics projects in Oxford. Computational support for researchers will be available through the Computational Biology Research Group (CBRG) at the WIMM and the Bioinformatics and Statistical Genetics (BSG) Group at the WTCHG.