Exploring_novel_applications_of_single_cell_genomics_in_parasites-sc-5904
Exploring_novel_applications_of_single_cell_genomics_in_parasites
One of the most unusual features of the Leishmania genome is that the number of copies of individual chromosomes varies extensively, both between strains and within the population of cells grown in vitro for a particular strain of this protist parasite. Whole-genome sequence data from pools of cells has established that this phenomenon is widespread, and microscopy-based approaches have shown that cells within a culture vary, but these are limited to investigating a few chromosomes at a time and therefore can never identify the somy profile across chromosomes of single cells, and cannot distinguish between local CNVs of the marker locus and whole-chromosome copy numbers. Genome-sequencing individual cells would improve on both techniques, and estimating the dosage of individual chromosomes does not require high-depth data. The chromium CNV platform thus seems ideally suited to investigating this phenomenon, allowing us to interrogate 100s-1000s of cells. We would like to perform replicate experiments from two cultures each of two strains to establish some baseline data on how quickly this 'mosaic' of aneuploidy evolves in culture, and how variable the distribution of aneuploidy is between two species. In parallel, we would like to investigate scRNAseq from the same populations of cells: Leishmania is unable to regulate transcription, so we expect (and have preliminary data from bulk cell transcriptomics) that RNA levels closely mirror the distribution of aneuploidy. These data will act as preliminary data for a fellowship application.  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/
Single-cell genome sequencing to understand clonal dynamics of aneuploidy in Leishmania