Genomics & Microfluidics: taking Cell Biology into the era of Big Data
Lead Research Organisation:
University of Edinburgh
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
The cell is one of few natural units in biology. Cell size, morphology and function vary greatly between types within an individual, among species, and in response to exogenous molecules (e.g. drugs) or mechanical stress or following genomic mutation, as in cancer. Current approaches commonly assess bulk populations of cells resulting in averaged data sets that hide potentially critical variations due to cellular heterogeneity in tissues or even within cells that may appear functionally equivalent by available phenotypic assays. Assaying many single cells is essential to understand biological phenomena that derive from stochasticity (e.g. lineage priming in development) or the cellular heterogeneity of tissues or tumours. It has only become feasible recently for thousands of single cells to be isolated and interrogated using the comprehensive, large-scale approaches afforded by microfluidics followed by DNA and/or RNA sequencing. Through a MRC Discovery Award, we seek to catalyse the investigation of cellular function across our two Universities by combining high-throughput microfluidics with big data ‘omics. The existing genomics and cell biology expertise in the University of Edinburgh (UoE) are perfectly complemented by Heriot-Watt University’s (HW) expertise in microfluidic engineering and mechanically stressing cells. A Discovery Award would catalyse a new cross-institutional venture, the Edinburgh Cellular Genomics Consortium (eCGC). Three PDRA positions would be funded across our two Universities to establish Droplet-based single cell sequencing technologies. Subsequently, these technologies and posts would be applied in three biomedical research collaborations selected by the eCGC Steering Committee. This application is distinct from normal response funding calls: Partnership Grant applications, for example, are not permitted to request PDRAs for scientific research.
Publications
Angermueller C
(2016)
Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.
in Nature methods
Baran-Gale J
(2018)
Experimental design for single-cell RNA sequencing.
in Briefings in functional genomics
Bedoya-Reina OC
(2017)
Functional RNA classes: a matter of time?
in Nature structural & molecular biology
Conway BR
(2020)
Kidney Single-Cell Atlas Reveals Myeloid Heterogeneity in Progression and Regression of Kidney Disease.
in Journal of the American Society of Nephrology : JASN
Crawford D.F.
(2018)
Fluorescence image morphology activated cell sorting (FIMACS)
in 22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2018
Crawford DF
(2017)
Image-based closed-loop feedback for highly mono-dispersed microdroplet production.
in Scientific reports
Dobie R
(2019)
Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis.
in Cell reports
Handel AE
(2018)
Comprehensively Profiling the Chromatin Architecture of Tissue Restricted Antigen Expression in Thymic Epithelial Cells Over Development.
in Frontiers in immunology
Handel AE
(2017)
Most brain disease-associated and eQTL haplotypes are not located within transcription factor DNase-seq footprints in brain.
in Human molecular genetics
Lopez-Baez JC
(2018)
Wilms Tumor 1b defines a wound-specific sheath cell subpopulation associated with notochord repair.
in eLife
Description | Human Cell Atlas Project |
Organisation | Broad Institute |
Country | United States |
Sector | Charity/Non Profit |
PI Contribution | Contributing scientific coordination and strategy to the international consortium. |
Collaborator Contribution | Contributing scientific coordination and strategy to the international consortium. |
Impact | None as yet. |
Start Year | 2016 |
Description | Organiser of Senescence UK 2019 Symposium |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | A relaxed and friendly forum for PhD students, postdocs and group leaders within the field to present their work and network |
Year(s) Of Engagement Activity | 2019 |
URL | https://www.ed.ac.uk/igmm/news-and-events/events/latest-events/senescence-symposium |