Genomics & Microfluidics: taking Cell Biology into the era of Big Data
Lead Research Organisation:
University of Edinburgh
Department Name: UNLISTED
Abstract
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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
Travnickova J
(2019)
Zebrafish MITF-Low Melanoma Subtype Models Reveal Transcriptional Subclusters and MITF-Independent Residual Disease.
in Cancer research
Teo YV
(2019)
Notch Signaling Mediates Secondary Senescence.
in Cell reports
Spektor A
(2017)
Cell Biology: When Your Own Chromosomes Act like Foreign DNA.
in Current biology : CB
Sesen M
(2020)
Image-Based Single Cell Sorting Automation in Droplet Microfluidics.
in Scientific reports
Sanchez-Pulido L
(2018)
TMEM132: an ancient architecture of cohesin and immunoglobulin domains define a new family of neural adhesion molecules.
in Bioinformatics (Oxford, England)
Regev A
(2017)
The Human Cell Atlas.
in eLife
Ramachandran P
(2019)
Resolving the fibrotic niche of human liver cirrhosis at single-cell level.
in Nature
Ponting CP
(2019)
The Human Cell Atlas: making 'cell space' for disease.
in Disease models & mechanisms
Owen R
(2018)
Single cell RNA-seq reveals profound transcriptional similarity between Barrett's oesophagus and oesophageal submucosal glands
in Nature Communications
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 |