Dear team,
There are three cell-annotation files (syn55219673, syn52363764, syn53694215) related to the Gene Expression (snRNAseq - DLPFC, Experiment 2) (syn31512863). What is the difference between the three? Also, the count matrices directory (syn51123521) has been updated recently. What has been changed?
Thanks in advance.
Best regards,
Rajesh
Created by rrajesh Thanks @gilad.green , @victor.baham , @lheath .
I appreciate your help. Hi @rrajesh,
We finished updating the Wiki explanations to include information about the 3 annotation files as well as the links to the manuscript and code. I'd suggest using them as follows:
* If you wish to investigate cell diversity - use the full-atlas file.
* If you wish to investigate associations related to the participants - use the n437 file.
Let me know if you have any other questions.
As for the count matrices directory - we only renamed the folder to better explain what is in that folder (compared to the raw and the cell type objects)
Best,
Gilad Green Hi @ppavlidis,
You can find the clinical metadata for all ROSMAP patients here: syn3191087. Join this to the cell annotation file by individualID contained in both the annotation file and the clinical metadata file. The clinical metadata will have a cognitive diagnosis category (cogdx), as well as some measures of neuropathology and demographics; you can check the data dictionary for ROSMAP data for full explanations of the clinical variables here: syn3191090.
Best,
Laura Hi @rrajesh,
Please see the updated folder wiki for [syn31512863](https://www.synapse.org/#!Synapse:syn31512863), particularly the **Single-nucleus RNA-seq analysis** section, for clarification about the difference between the three cell-annotation files. Additionally, as Laura mentioned, the count matrices directory has only been renamed to more aptly describe its contents at the request of the data contributor.
Thank you,
Victor Hi team,
I would like to follow up and ask about the cell-annotation.n424.csv file (syn52363764). Unfortunately, the file does not include pathological diagnosis (AD vs non-AD) of the individual IDs referenced in the publication. I would appreciate your guidance on how to access such information.
Best,
Paul Hi @rrajesh,
I can see that the cell-annotation.n424.csv file (syn52363764) is the one that is officially associated with a recent [publication](https://www.nature.com/articles/s41588-024-01685-y) examining this data, but I don't know where the other two came from. I am tagging the people who contributed these three cell annotation files: @masashi and @gilad.green, could you please clarify how these three cell annotation files differ? Thank you for your help!
The count matrices directory was updated recently but the files themselves have not been updated. The directory update was likely due to some administrative or organizational change and won't affect the data in any way.
Best,
Laura
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