Hello,
I may be mistaken, however, I can't find any processed snRNA seq data from the Zhou Nat Med 2020 study available (meaning normalised count matrix with associated meta data, e.g. cell type)? We have obtained authorisation as required, however, I have the impression that there are only "unprocessed" gene expression files on the AD knowledge portal.
Thank you very much in advance!!!
Stergios Tsartsalis
Created by stergios20 Great! Glad to help. Excellent, file retrieved!
Thanks so much for your patience and help.
-steve The information about the data analysis can be found in the [AD Knowledge Portal](https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage?Study=syn21670836) under Methods: Gene Expression (Clustering). The file itself is the only analysis file that appears in the Study Data table. Clicking on the '1' under the column Files will take you [to the query for the file](https://www.synapse.org/#!Synapse:syn11346063/tables/query/eyJzcWwiOiJTRUxFQ1QgKlxuICBGUk9NIHN5bjExMzQ2MDYzXG4gIFdIRVJFICgoKCgoYHN0dWR5YCBMSUtFICclc25STkFzZXFBRF9UUkVNMiUnKSBBTkQgKChgZGF0YVN1YnR5cGVgIDw+ICdtZXRhZGF0YScpIE9SIChgZGF0YVN1YnR5cGVgIElTIE5VTEwpKSkgQU5EIChgcmVzb3VyY2VUeXBlYCA9ICdhbmFseXNpcycpKSBBTkQgKGBkYXRhVHlwZWAgSVMgTlVMTCkpIEFORCAoYGFzc2F5YCA9ICdzY3JuYVNlcScpKSIsICJvZmZzZXQiOjAsICJsaW1pdCI6MjV9), where you can download the file. This file is currently not in the data updates section, but will be included in these notes under the next release (17.1) that will be coming out soon. Hi @nicole.kauer ,
Thank you for facilitating the data update, it should prove very helpful to the broader research community.
I'm sorry, though, but I'm having a difficult time being able to find exactly where this new nuclei-level metadata is. I've been poking around the different data directories I see at the AD Knowledge Portal Study Page, as well as through details in the [data updates](https://adknowledgeportal.synapse.org/News?cat=4) section.
Could you please provide a direct link to the file, or perhaps some instructions now how to navigate to where this exact file is?
I'm sorry if I'm missing something obvious, and thank again for all of your help wit this.
-steve @stergios20 and @slianoglou, this data is now available. Please see the [AD Knowledge Portal Study Page](https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage?Study=syn21670836). Thank you very much!! @slianoglou , I have been working with the original authors to get the cellType data so that is in the works. As for the extra items, I did not see that the comment was edited to add those. I am not sure I will be able to get that information, but I can ask. Hi @nicole.kauer, any luck trying to get these data from the original authors? Perhaps it be helpful if we tried contacted them individually?
Thanks,
-steve
@nicole.kauer that would be great, thanks Nicole!
(Edited to add):
Just to be a bit less ambiguous, it would be super helpful if the authors could add more than just the cell-type classification per cell, such as the the cell-level subclustering labels.
For instance, in Fig 4i they show the 7 re-clustered microglia populations (Micro0, ..., Micro6).
Likewise, in Fig 5a we see a reclustering of the astrocyte cells (Astro0, ..., Astro4).
If they could provide that level of metadata for these snRNAseq, it would be most helpful.
Thanks again! @slianoglou, the metadata we have on the specimens can be found at [syn21738956](https://www.synapse.org/#!Synapse:syn21738956). However, there are no cell types noted in this metadata file. I will contact the contributor and see if this information can be made available. Is there any update on if the snRNA-seq cell-level annotations use in the paper can be made available (ie. like celltype annotations)? Apologies in advance if they have been, and I just haven't able to find it.
Thanks!
I will look into why the AD Knowledge Portal is not surfacing the processed data. In the meantime, the count matrices can be found [here at syn21126462](https://www.synapse.org/#!Synapse:syn21126462).
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