Cell type markers for neuronal organoid cells of developing brain


I’m studying single cell transcriptomics data set of developing neuronal organoids and wondering if there is a way to identify a list of marker genes for the developing immature and mature neuronal cell types. I find that transcriptomics_explorer and cell type knowledge explorer are quite useful for navigation, but I am not sure a couple of points:

  • If these tools could be directly used for the developing neurons as well although these are likely for the adult cell types?
  • If there is another good source within the Allen Brain Map database or anywhere else?

Any helps would be great as I’m new at this field. Thanks in advance!


Hi @junha-shin,

Thanks for your interest in these tools! Both the Transcriptomics Explorer and Cell Type Knowledge Explorer are only focused on adult brain, so you’ll probably need to look elsewhere for your work. Both the BrainSpan Atlas of the Developing Human Brain and the NIH Blueprint Non-human Primate Atlas include components focused on primate development. Specifically, both have microarray-based atlases where cortical layers (and other anatomic structures) were microdissected in prenatal time points, which might be useful for you. If you are looking for single cell/nucleus RNA-seq efforts, here is an example in the UCSC Cell Browser from another group. There are almost certainly other or newer ones that I’m unaware of.