# Is there a cell type taxonomy of mouse in the hippocampus?

**URL:** <https://community.brain-map.org/t/is-there-a-cell-type-taxonomy-of-mouse-in-the-hippocampus/4268>\
**Category:** Technical\
**Tags:** how-to\
**Created:** [March 19, 2025, 9:44am UTC](https://community.brain-map.org/t/is-there-a-cell-type-taxonomy-of-mouse-in-the-hippocampus/4268 "2025-03-19T09:44:29Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![YSivannn](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/ysivannn/32/2180_2.png) [@YSivannn](https://community.brain-map.org/u/YSivannn)\
**Post date:** [March 19, 2025, 9:44am UTC](https://community.brain-map.org/t/is-there-a-cell-type-taxonomy-of-mouse-in-the-hippocampus/4268/1 "2025-03-19T09:44:29Z")

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Hi there,

I am analyzing gene expression across different cell types, such as excitatory and inhibitory neurons. However, I am quite confused because the taxonomy for excitatory and inhibitory neurons is only provided for the cortex in the Allen Brain Atlas, but not for the hippocampus. Is there any reference available for the cell type taxonomy of the mouse hippocampus in the Allen Brain Atlas?

Thanks a lot！

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**Author:** ![jeremyinseattle](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/jeremyinseattle/32/50_2.png) [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)\
**Post date:** [March 19, 2025, 2:42pm UTC](https://community.brain-map.org/t/is-there-a-cell-type-taxonomy-of-mouse-in-the-hippocampus/4268/2 "2025-03-19T14:42:40Z")

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I would recommend one of two strategies:

1. Subset the Mouse Cortex + Hippocampus taxonomy to only include hippocampus, as described **[in this post](https://community.brain-map.org/t/cell-types-database-rna-seq-data/4246)**
2. Subset the whole mouse brain taxonomy to only include hippocampus. The basic strategy would be the same–if interested, I’d suggest reviewing **[the ABC Atlas Access Jupyter notebooks](https://alleninstitute.github.io/abc_atlas_access/intro.html)**

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**Author:** ![YSivannn](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/ysivannn/32/2180_2.png) [@YSivannn](https://community.brain-map.org/u/YSivannn)\
**Post date:** [March 20, 2025, 10:43am UTC](https://community.brain-map.org/t/is-there-a-cell-type-taxonomy-of-mouse-in-the-hippocampus/4268/3 "2025-03-20T10:43:15Z")

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Thank you very much! I still have some confusion regarding the gene expression data in the _Whole Cortex & Hippocampus - 10x Genomics (2020)_ dataset. Specifically, does the value in the _“Gene Expression by Cluster (trimmed means)”_ matrix represent TPM, or was it calculated using a different method? Is there any official documentation that explains how the expression values were processed in the Allen Brain Atlas? I appreciate your help!

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**Author:** ![jeremyinseattle](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/jeremyinseattle/32/50_2.png) [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)\
**Post date:** [March 20, 2025, 3:38pm UTC](https://community.brain-map.org/t/is-there-a-cell-type-taxonomy-of-mouse-in-the-hippocampus/4268/4 "2025-03-20T15:38:27Z")

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Hi @YSivannn,

Your best best on documentation will be to [review the May 2021 manuscript in Cell](https://www.sciencedirect.com/science/article/abs/pii/S0092867421005018?dgcid=rss_sd_all). The great majority of our single cell/nucleus RNA-seq data sets (including this one) are normalized by taking log2([counts per million]+1). This log normalizes the data but also scales things so that 0 = no expression. Trimmed means takes the value of all cells for a given cluster that fall between the first and third quartile, and averages them.

Best,  
Jeremy

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**Author:** ![YSivannn](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/ysivannn/32/2180_2.png) [@YSivannn](https://community.brain-map.org/u/YSivannn)\
**Post date:** [March 20, 2025, 3:54pm UTC](https://community.brain-map.org/t/is-there-a-cell-type-taxonomy-of-mouse-in-the-hippocampus/4268/5 "2025-03-20T15:54:07Z")

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Hi Jeremy,

Thank you for the clarification! That really helps. I’ll check out the manuscript.

Best,  
Sivan