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

Cell Taxonomies
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1

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!

Anna

2

Hi Anna,

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

https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-smart-seq

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 alleninstitute.org

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

Thank you