Hi, Wondering if anyone knew what the cell states ex: Mic.1, End.2, etc in the cell_annotation.csv file mapped to. Usually different numbers, Mic.1, Mic.2 refer to different states in different studies and is there something I can reference to find what each number represents? Thanks!

Created by leo13692
Hi @lheath and @leo13692, Cell states have been annotated by our collaborator Gilad Green and Naomi Habib and have several versions. The [eQTL preprint](https://doi.org/10.1101/2022.11.07.515446) and syn51218314 use "version 1" annotation. Our [atlas preprint](https://doi.org/10.1101/2023.03.07.531493), which uses "version 2" annotation, discusses biological details of the clusters. Recently, Gilad made "version 3" annotation. Both preprints and syn51218314 will be updated soon using this latest (and probably final) annotation. Best, Masashi
Hi @leo13692, The investigators who generated this data uploaded it into synapse before publication, so at the moment, to my knowledge, the cell states/finer subclusters generated for this dataset (i.e. Mic.1, Mic.2, etc) have not been characterized. Based on the [preprint](https://www.biorxiv.org/content/10.1101/2022.11.07.515446v1.full) associated with this data set, it seems to me that these cell states were determined by the authors, and were not based on any labels generated in other studies (see 'Methods: Cell Type Classifications" in the preprint, though the methods for defining cell subclusters is not terribly detailed yet). I am tagging @masashi to confirm: hi masashi, were the cell subclusters labeled in [syn51218314](syn51218314) based on any existing nomenclature, or were they identified within the parameters of this particular dataset only? Are there any resources characterizing these subclusters yet? Thank you! Best, Laura

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