Studying the transcriptome of organisms allows for the characterization of different aspects of development and disease progression. Studies of this kind are usually done with large numbers of cells, giving an expression profile that serves as an overview of that cell type or tissue. In this thesis, two different transcriptomic studies were done with small populations of cells and with single cells. To examine the immune response of a hSOD1G93A Amytrophic Lateral Sclerosis (ALS) mouse model, small populations of cells were analyzed by microarray using a protocol modified from one developed by Trimarchi et al (2007) to study single cells. Multiple genes were found to be significantly differentially expressed between mutant and wild-type ALS mice that with further study will lead to a better understanding of the immune response's role in this disease. To study the development of the enteric nervous system in zebrafish, single enteric neurons were isolated from 7 day post fertilization (7 dpf) and 48 hour post fertilization (48 dpf) zebrafish larvae and prepared for RNA sequencing analysis. There are no sequencing results yet, but preliminary data suggests that different subtypes of enteric neuron precursors were isolated from 48 hpf larvae, and that both differentiated enteric neurons and enteric neurons undergoing differentiation were isolated from 7 dpf larvae. This study should expand our knowledge of signaling pathways and other genes involved in migration, proliferation, and differentiation of the ENS, as well as identify specific markers of precursors and enteric neurons.