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Publicly Available CyTOF Data With Annotated Cell Types
Posted:
Tue Jul 02, 2024 7:17 pmby bumpCyto
Hello,
Does anyone have nice examples of publicly available (and somewhat recently generated) CyTOF datasets with cell type annotations?
Also, has anyone else had issues with FlowRepository recently?
Thanks!
Re: Publicly Available CyTOF Data With Annotated Cell Types
Posted:
Tue Jul 02, 2024 7:58 pmby mleipold
Hi Eric,
What are you looking for when you say "with cell type annotations"?
What issues are you having with FR? I hadn't tried downloading anything lately, just some dataset searches. However, I can confirm that I'm currently (1PM PST Tues 7/2/24) unable to download even a single file from FR.
For example:
http://flowrepository.org/experiments/7 ... iped_filestrying to download even the Media control file results in a "An error occurred while communicating with the server. You may want to refresh the page (F5) and try again." error. I'm on a Mac, but it's occurring both on Firefox and Chrome.
Mike
Re: Publicly Available CyTOF Data With Annotated Cell Types
Posted:
Wed Jul 03, 2024 6:05 amby sgranjeaud
Hi,
I confirm that since a few week-end I did not succeed in downloading a single file from FR. I was about posting when I saw your message.
The javascript usually says there is an error when connecting to the server and aks for reloading the page, which does not change anything. When there is no connection error, the zipping of files never end in my hand.
It would be great if an temporary alternative is proposed.
Best,
Samuel
Re: Publicly Available CyTOF Data With Annotated Cell Types
Posted:
Wed Jul 03, 2024 3:20 pmby bumpCyto
Thanks Mike.
I'm interested in datasets where the cells have been grouped into general types by the original authors (e.g. NK, CD4+ T, etc.)
Eric.
Re: Publicly Available CyTOF Data With Annotated Cell Types
Posted:
Wed Jul 03, 2024 4:50 pmby mleipold
Hi Eric,
I don't think I'm aware of any publicly available datasets like you describe (eg, both LiveIntactSinglets FCS files, as well as all the daughter manually-gated FCS files).
Mike
Re: Publicly Available CyTOF Data With Annotated Cell Types
Posted:
Wed Jul 03, 2024 4:54 pmby teikoramji
Not sure if this is what you're looking for, but we have a mass cytometry dataset like this:
https://app.teiko.bio/projects/UMN002/overview. You should be able to export the FCS files from the "Data Export" field.
Re: Publicly Available CyTOF Data With Annotated Cell Types
Posted:
Thu Jul 04, 2024 4:56 pmby bumpCyto
bumpCyto wrote:Hello,
Does anyone have nice examples of publicly available (and somewhat recently generated) CyTOF datasets with cell type annotations?
Also, has anyone else had issues with FlowRepository recently?
Thanks!
teikoramji wrote:Not sure if this is what you're looking for, but we have a mass cytometry dataset like this:
https://app.teiko.bio/projects/UMN002/overview. You should be able to export the FCS files from the "Data Export" field.
Thanks!
Is it possible to line up the .fcs files with the cell types? I was able to download the .fcs files in a zip, and I see that there is a gated_cell_state file that contains cell types, but it is not clear to me how to match the two files.