# Deconvolution of mice bulk hippocampal transcriptomics

**URL:** <https://community.brain-map.org/t/deconvolution-of-mice-bulk-hippocampal-transcriptomics/4812>\
**Category:** Transcriptomics Explorer\
**Created:** [December 17, 2025, 11:15am UTC](https://community.brain-map.org/t/deconvolution-of-mice-bulk-hippocampal-transcriptomics/4812 "2025-12-17T11:15:22Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![lciaran](https://avatars.discourse-cdn.com/v4/letter/l/4491bb/32.png) [@lciaran](https://community.brain-map.org/u/lciaran)\
**Post date:** [December 17, 2025, 11:15am UTC](https://community.brain-map.org/t/deconvolution-of-mice-bulk-hippocampal-transcriptomics/4812/1 "2025-12-17T11:15:22Z")

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Hi! I have performed bulk hippocampal transcriptomics in mice and I’m interested in performing deconvolution to separate the different cell types. Is there a suitable database which I can use as my matrix and which method of deconvolution would you recommend? Thank you!

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**Author:** ![zizheny](https://avatars.discourse-cdn.com/v4/letter/z/f9ae1b/32.png) [@zizheny](https://community.brain-map.org/u/zizheny)\
**Post date:** [January 12, 2026, 6:31pm UTC](https://community.brain-map.org/t/deconvolution-of-mice-bulk-hippocampal-transcriptomics/4812/2 "2026-01-12T18:31:30Z")

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ABC atlas can serve as a good reference for your study. You can find instruction for accessing the data here: [GitHub - AllenInstitute/abc\_atlas\_access: Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas](https://github.com/AllenInstitute/abc_atlas_access)

Particularly, cellxgene matrix and metadata for HPF (hippocampal formation) can be found here:

[https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression\_matrices/WMB-10Xv3/20230630/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/WMB-10Xv3/20230630/)

You might want to further subset based on roi information, or by cell types based on their spatial location determined by MERFISH.

We don’t have much hands-on experience with the bulk deconvolution, so couldn’t give you much advice. You might find this website useful, which provides substantial resources on this topic:

> **[22. Bulk deconvolution — Single-cell best practices](https://www.sc-best-practices.org/deconvolution/bulk_deconvolution.html)**