Stem cells exist within complex environments, surrounded by other cells. This presents a technical challenge to researchers that want to study gene expression in stem cells without removing the cells from their natural environment. We have developed a technology that makes this possible. We used the RABT technique to purify mRNAs (gene products) from stem cells of the immune system and the nervous system, in a way that was not previously possible. We have also optimized this technique for studies in various model systems, including various tissues and developmental stages in mouse models. The tools and methods we developed should be useful to scientists in many disciplines and will allow identification of genes that regulate stem cell behavior.