Platforms and Training
The single cell technology platforms available through the OSCBC are housed in two facilities based at the MRC WIMM and WHG, 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.
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 WHG and MRC WIMM facilities house Fluidigm BioMark platforms for high throughput single-cell or low cell number QPCR analysis. The MRC WIMM facility also houses a nanoString platform which can be used for targeted gene expression analysis of single cells.
Microfluidic Cell Capture
Both the WHG and WIMM facilities provide access to 10X Genomics for the large-scale isolation and analysis of single cells, including methods for whole-transcriptome and T cell receptor and B cell receptor analysis on hundreds to thousands of cells per sample. The WHG facility houses the 10X Chromium platform which can also run 10X linked-reads protocols for genomic (not SC) sequencing.
Both the WHG and MRC 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 WHG 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.
Both the WHG and MRC 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 WHG and MRC WIMM facilities have established workflows for whole genome amplification of FACS isolated single-cells.
Automated Liquid Handling
Both Single Cell Facilities house a number of platforms for precise and repeatable nanolitre liquid handling inclusing the Mosquito (MRC WIMM), Labcyte Echo (WHG) and Beckman robotic liquid handling platforms (MRC WIMM and WHG).
The Wolfson Imaging Centre was established in 2012 with funds received from the Wolfson Foundation. The facility contains a number of platforms suitable for single-cell imaging.
Next generation sequencing platforms are available at the MRC WIMM (MiSeq and NextSeq500) and WHG facilities (HiSeq 2500, HiSeq 4000, NextSeq 500 and MiSeq).
The MRC WIMM Mass Cytometry 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.
The MRC 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.
The OSCBC provided funding to establish the new, purpose built MRC WIMM Centre for Computational Biology. The Centre includes computational scientists with a range of expertises in bioinformatics, statistical genetics, imaging and analysis of data from single cells. The Centre also provides the necessary infrastructure (storage and server capacity) through a centralized computational resource that supports single cell genomics projects in Oxford. Computational support for researchers is available through the the MRC WIMM Centre for Computational Biology and the Bioinformatics and Statistical Genetics (BSG) Group at the WHG.