Single_cell_gene_expression_patterns_across_different_cell_cycle_stages_in_mouse_embryonic_cells

Progression through the cell cycle is accompanied by transcriptomic changes as cells move through the different cell cycle stages (from G1 to S to G2/M). Single cell RNA-sequencing experiments capture individual snapshots of cells at different cell-cycle stages, which are averaged in traditional bulk RNA-sequencing experiments. It is a major challenge for the interpretation of single cell RNA-sequencing data to assign individual cell-cycle states and their transcriptional signature. Being able to assign cell cycle stage is important for two reasons: (i) to remove unwanted gene expression variation due to simple cycling and (ii) to be able to discover correlations between the cell cycle and other processes, such as differentiation. We propose to address this problem by sorting cells into different cell cycle stages. This data will allow us to develop approaches to assign cell cycle stage from a pool of cells.