A platform for transcriptome time-series in single cells with applications to hematopoietic stem cells

We will integrate live time-lapse imaging with genome-wide sequencing of RNA and chromatin, where one sister cell is harvested at every division in low-stress environments with exceptional uniformity in time and space. This provides vertical transcriptome time-series along lineages of single cells, while also providing information about growth, morphology and spatiotemporal reporter dynamics. We established feasibility of all key steps. As a proof-of-principle application we will use the platform to establish long-term maintenance, expansion and monitoring of primary tissue cells -- a ‘holy grail’ in regenerative biology and cell-based therapies. Specifically, we will expand hematopoeitic stem cells in culture for transplantation, while continuously tracking cell states along the lineages. If successful, this pilot will set the stage for optimizing additional stem cell and immunotherapy protocols, and produce (1) a commercializable research platform, (2) derivative methods to expand cells for therapy, and (3) cellular products that result from them.