Cellular differentiation can be studied by introducing an inheritable marker into stem cells that pass on this tag to their progeny during differentiation. In combination with kinetic measurements, differentiation rates can be derived. Using such approaches, we studied fundamental properties of blood forming (hematopoietic) stem cells (HSCs) in the bone marrow of mice, which led to estimates on frequencies of HSCs contributing to hematopoiesis, and on differentiation rates: Many HSCs contribute, each one is rarely active and produces under normal steady state conditions only low output. These experiments were all based on the propagation of a single color label, a fluorescent protein, which falls short of revealing which sort of lineage was generated by the HSCs. This is because all cell types can only have the same color. We therefore developed a new, highly versatile barcoding system, termed Polylox, which makes it possible to introduce several hundred thousand different genetic barcodes into cells. The advantage of this DNA recombination system is that it is inducible by Cre recombinase, which enables the barcode generation to be controlled in terms of time and tissue. Polylox can be used to determine which cell lineages arise from individual HSC clones (fate analysis), and via which routes blood and immune cells emerge (analysis of hematopoietic structure). With the aim of opening the door for the coupled analysis of fates (barcoding) and transcriptome (RNA sequencing), we have developed a new version of Polylox, termed PolyloxExpress. Here, barcodes are expressed as RNA molecules and can therefore be read together with the transcriptome. Collectively, applying these new barcoding technologies, we have generated data towards the deconvolution of stem cell functions and hematopoiesis, including analysis of the origins of highly diverse immune cell lineages under physiological and stress conditions.