This method is well-suited to the temporal framework of our data, which is essentially a snapshot in time of a dynamic system, and was stable against small perturbations in our dataset, converging to the k-means solution. Although AIC itself is poorly suited to traditional null hypothesis testing, multiple methods have been developed to evaluate uncertainty in model selection. Application of these information theoretic measures to examine differences among the canonical 1-cluster model, the optimal model, and other cluster arrangements, supports the conclusion that these highly purified cells exist in distinct subpopulations rather than as one homogeneous population. We therefore establish the effectiveness and relevance of our large-scale computational method by demonstrating non-random, BEPP monohydrochloride transcriptionally defined subpopulations that have not previously been described within the well-studied and putatively homogenous murine LT-HSC cell population. Our results demonstrate the feasibility of measuring gene expression in multiple individual cells from a stem cell population using single cell qPCR in a multiplexed array based on microfluidic large-scale integration technology. Using this approach, we detected variations in gene expression profiles within a well-studied murine LT-HSC population that could not be accounted for by stochastic transcriptional noise alone. Specifically, we identified several transcriptionally defined subpopulations that were consistent with the known functional heterogeneity of LT-HSCs. It is important to note that post-transcriptional factors such as mRNA translation or protein modification may serve to mitigate the impact of this heterogeneity. In addition, these results will have to be confirmed with empirical testing of the functional differences displayed by the HSC subpopulations we describe here. This will require the CHIC-35 identification and application of new sorting parameters to prospectively isolate these subpopulations. Given the observed variations in gene expression, this search is warranted, as the development of new sorting parameters may permit further enrichment of hematopoietic stem cells. More broadly, these findings demonstrate the utility of such an approach to define the transcriptional organization of complex cell populations on a tissue and organ level.