The primary NSCs were isolated from the newborn C57BL/6J mice within 24 h， and were expanded and purified by passage. The morphology of cells was observed； the expressions of Nestin and Sox2 were detected by immunofluorescence method；the differential proteins of NSCs in hypothalamic and hippocampal tissues were analyzed by tandem mass tag （TMT） proteomics， and the obtained differential proteins were analyzed by bioinformatics analysis.

The morphology detection results showed that the NSCs in hypothalamic and hippocampal tissues presented the typical neurosphere morphology with opacity and high refractive index. The immunofluorescence detection results showed that the positive expression rates of Nestin and Sox2 in the NSCs in hypothalamic and hippocampal tissues were increased with the increase of culture generation， and it reached over 98% in the 4th generation， but the difference in the NSCs between hypothalamic and hippocapal tissues was not statistically significant（P>0.05）. The proteomics analysis results showed that compared with the hippocampal tissue，the expression levels of 6 kinds of proteins in the NSCs in hypothalamic tissue were significantly increased（P<0.05 or P<0.01）， while the expression levels of 4 kinds of proteins were significantly decreased（P<0.05 or P<0.01）. The gene ontology （GO） analysis results revealed that the differential proteins were mainly involved in 8 biological processes such as negative regulation of dopamine uptake involved in synaptic transmission， 6 kinds of molecular functions such as rRNA （guanine） methyltransferase activity and so on， and 6 cellular components such as integral component of Golgi membrane and so on. The Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway analysis results revealed that the differential proteins were mainly involved in 7 signaling pathways such as SNARE interactions in the vesicular transport and so on.

The primary NSCs in hypothalamic and hippocampal tissues from C57BL/6J mice which are cultured in vitro have no differences in morphology and the expressions of NSCs markers. The expressions of certain specific proteins are different，the differentially expressed proteins mainly play a role in synaptic transmission， vesicle transport， and metabolism and may play an important role in the orientation differentiation and functional specificity of NSCs in different regions.