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

**URL:** <https://community.brain-map.org/t/top-leaf-classification-possible-for-mouse-whole-cortex-and-hippocampus-smart-seq-rnaseq-data/1828>\
**Category:** Cell Taxonomies\
**Tags:** atlas-cell-types, mouse, rna-seq\
**Created:** [September 2, 2022, 8:28am UTC](https://community.brain-map.org/t/top-leaf-classification-possible-for-mouse-whole-cortex-and-hippocampus-smart-seq-rnaseq-data/1828 "2022-09-02T08:28:27Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![AnnaGalakhova](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/annagalakhova/32/681_2.png) [@AnnaGalakhova](https://community.brain-map.org/u/AnnaGalakhova)\
**Post date:** [September 2, 2022, 8:28am UTC](https://community.brain-map.org/t/top-leaf-classification-possible-for-mouse-whole-cortex-and-hippocampus-smart-seq-rnaseq-data/1828/1 "2022-09-02T08:28:28Z")

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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

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**Author:** ![Susan.Sunkin](https://avatars.discourse-cdn.com/v4/letter/s/6a8cbe/32.png) [@Susan.Sunkin](https://community.brain-map.org/u/Susan.Sunkin)\
**Post date:** [October 4, 2022, 4:02am UTC](https://community.brain-map.org/t/top-leaf-classification-possible-for-mouse-whole-cortex-and-hippocampus-smart-seq-rnaseq-data/1828/2 "2022-10-04T04:02:17Z")

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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](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fportal.brain-map.org%2Fatlases-and-data%2Frnaseq%2Fmouse-whole-cortex-and-hippocampus-smart-seq&data=05%7C01%7C%7Cc884b368b0cc45e6a0dd08daa5b9f86e%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C0%7C638004515409350525%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=84SBY6QdM5Rm7GDyylbqg6uFpWjsz1OqqQ1eCOohGtk%3D&reserved=0)

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](http://alleninstitute.org)

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

Thank you