New_genetic__imaging_and_microfluidics_technologies_for_single_cell_genomics______. New_genetic__imaging_and_microfluidics_technologies_for_single_cell_genomics______

There are two major limitations to single cell genomics at present: first, information about the lineage relationships between cells and their locations within tissues is lost during cell disaggregation, and second, throughput is limited, increasing cost. Even the most advanced cell handling technologies (e.g. the Fluidigm C1) currently limit throughput to, at best, hundreds of cells, at significant expense in instrument, consumables, and operator time. Miniaturising single cell analysis further to nano- to pico-litre microdroplet compartments paves the way to much higher throughput (on the order of 104 to 106) so that handling steps are no longer limiting. Such devices are cheap and easy to operate, lowering the bar for widespread use of this technology. In addition, information about lineage and cellular context within tissues would allow one to ask questions about diversification of cell types, interactions between different cell types or how location influences transcriptional profile. We have funding from the Wellcome Trust to develop a novel approach to uniquely barcode cells so that their lineage and spatial relationships can accurately and easily be reconstructed. This genetic fluorescent barcoding will be combined with imaging and microfluidics to develop a cheap high- throughput platform for single cell genomics that retains cell lineage and location data. At various points during the course of the project, fluorescent imaged mouse embryos will be disaggregated into single cells (in the University of Oxford) and then sent to the WTSI to be processed for transcriptome sequencing. Mid way through the project, a microfluidic rig will be built in the WTSI and will be used to sort single cells and process them for sequencing. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/