Analysis of a single cell by definition gives much more precise information about mechanisms of cellular processes than analysis of a homogenate sample of many individual cells. This challenges the development of new technologies for single cell analysis. Major part of the studies at the single cell levels is devoted to analysis of transcriptome that allows to identify the key players. In the present review we discuss major possible approaches and steps for analysis of a single-cell transcriptome: methods of cell isolation, RNA isolation and amplification of the sample content, ways for qualitative, quantitative and spatial analysis of transcripts in the nervous cell. Special attention is given to genome-wide RNA-seq, expression analysis methods and application to neurobiological research, including molecular mechanisms of synaptic plasticity.
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