Citation for Allen scRNAseq Mouse and Human datasets


I have downloaded and re-analyzed the pan-GABAergic, pan-glutamatergic scRNAseq dataset derived from mouse hippocampus and cortex, obtained from the Allen portal:

I have used this as a reference for comparing it with several in-house datasets using Seurat.

I would like to know

  1. all the appropriate Allen Brain publications that utilize this dataset, and
  2. all the GEO accession numbers
    corresponding to this dataset, for accurate citation.

Thanks and regards,

Hi @vivek.mahadevan,

A paper on mouse hippocampus and cortex is in the works, so stay tuned. In the meantime, I would suggest you consider citing the Allen Institute’s previous work on mouse cell types in primary visual cortex. As always, we encourage following our citation policy. I’m not sure what (if any) components of this work are stored in GEO or in the BCDC portal, so hopefully someone else will reply.


Hi @vivek.mahadevan,

There is a longer post about how to cite data from the datasetrs on here:
How do I cite information from the Allen Brain Atlas website?
Glad to hear the data is useful!

Thanks for your reply Jeremy! Much appreciated.

Thanks @brain