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A complex gene-expression network underlies neural stem cell (NSC) differentiation, and regulated patterns of microRNAs are predicted to participate in deciding cell fate. We compared microRNA and mRNA profiles from NSC to identify interactions between gene-expression and non-coding RNA networks. Two NSC cell clones were tested; one was differentiated primarily into glutamatergic neurons upon bFGF withdrawal, and one was more multipotential. Regulated microRNAs were quantified using NCode microarrays, and mRNAs were detected using the ABI1700 rat genome arrays. Significantly regulated RNAs were confirmed by qPCR. Cross-correlation studies demonstrate the presence of embedded patterns of regulated mRNAs and microRNAs exhibiting either positive or negative correlation. Focusing on transcription factor mRNAs, we confirmed specific examples of microRNA inhibition of translation in a subset of those predicted by computational algorithms. Furthermore, specific micro-RNAs are transcriptional targets of regulated transcription factors. These results indicate the existence of a complex regulatory network involving both transcriptional and post-transcriptional events during NSC differentiation.