SCN 3D Atlas

SCN 3D Atlas

The suprachiasmatic nucleus (SCN) is the master circadian pacemaker in mammals. SCN is a heterogeneous nucleus composed of a variety of cell types. These different cell types may have different spatial localizations in SCN. In the mouse, SCN was usually simply divided into two subdivisions: a ventral “core” region and a dorsal “shell” region. There was no physical boundary between core and shell but they can be distinguished by their neurochemical contents. Some studies also revealed the difference between anterior and posterior part of SCN. In order to make better use of the three-dimensional SCN coordinate system and facilitate academic exchanges and sharing, we established this website, http://yanlab.org.cn/scn-atlas/, based on WebGL (Web Graphics Library) technology, which can be used to present our 3D data. You can browse AVP/VIP/CCK/GRP domain here. You can also see the spatial distribution of specific cre-line-defined SCN subtypes (from each single tissue clearing experimental trial). Furthermore, you can search for the gene of interest,  then you can get access of the spatial expression pattern of the gene in SCN region (from LCM-seq). 

This part of data has been published on:

Wen S, Ma D, Zhao M, Xie L, Wu Q, Gou L, Zhu C, Fan Y, Wang H, Yan J. Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus. Nat Neurosci. 2020 Mar;23(3):456-467. doi: 10.1038/s41593-020-0586-x. Epub 2020 Feb 17. PMID: 32066983.