Top Leaf classification possible for Mouse Whole Cortex and Hippocampus (SMART-seq) RNAseq data?

Hello everyone.
I am trying to get RNAseq data from Mouse Whole Cortex and Hippocampus (SMART-seq) database.

My interest is to look at the differential expression of a gene between three major excitatory subclasses in mouse L2/3 - L2/3 IT VISp Rrad, L2/3 IT VISp Adamts2, L2/3 IT VISp Agmat (Berg et al, 2021).

Although in the metadata this information is not accessible. What you can select, is a subclass_label - L2/3 IT CTX. This indeed helps to find gene expression for these types, but not the difference between them.
There is also a subclass_order, which is an order of the subclass in Transcriptomic Explorer, but these types are not there either. I tried to find anything which would connect the types I am interested in with subclass_order, but I failed.

Does anyone know if this is possible at all to select RNAseq data based on specific cell types, as in the human dataset, or not?

Thanks in advance!


Hi Anna,

Sorry for the delay in the response. You can download the whole Smart-seq data from

and I would like to send you a list of samples which are mapped to these clusters (Tasic 2018)

L2/3 IT VISp Rrad, L2/3 IT VISp Agmat, L2/3 IT VISp Adamts2.

Could you email me at susans
then @
followed by

so I can email you a file. The file format is not supported in this forum.

Thank you