Combined single-cell tracking and omics improves blood stem cell fate regulator identification

HSCs can undergo asymmetric lysosomal division, marking the daughter receiving less lysosomes for metabolic activation and its corresponding sister for quiescence (Loeffler et al. 2019, Nature). We use scRNA-Seq to trace the earliest fate regulators controlling this fate divergence in HSC daughter cells. Methods: We use quantitative time-lapse imaging of murine HSCs to detect their first in-vitro division. Cells are isolated with a micromanipulator and submitted to Smart-Seq2 RNA sequencing. Single-end reads were mapped to the M 21 release mouse genome using STAR aligner. Raw Counts are extracted with featureCounts. Results: We successfully isolated 474 high-quality single cell transcriptomes from HSC daughter cells and mapped their transcriptional profiles to the observed inheritance. Single-cell mRNA profiles of HSC daughters isolated from 12–19 week old, male C57BL/6JRj mice. We use quantitative time-lapse imaging of murine HSCs to detect their first in-vitro division. Cells are isolated with a micromanipulator and submitted to Smart-Seq2 RNA sequencing with their inheritance and relationship recorded. To match raw read files to paired daughter cells, use the metadata .csv files provided. Daughter cells share the same 'Movie', 'Experiment', 'Position' and 'Colony'. The column 'LysosomeInheritanceLabel' identifies each daughter cell in the pair as either having received less or more lysosomes than the corresponding other sister. Fastq names can be retrieved from the column 'FastQNames'.