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Useful to have list of CyTOF datasets?

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mleipold

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Location: Stanford HIMC, CA, USA

Post Mon May 14, 2018 4:28 pm

Useful to have list of CyTOF datasets?

Hi all,

More and more labs are publishing new CyTOF datasets, and more and more labs are reusing previously-generated datasets for algorithm development and comparison.

Would it be useful for the community to have a list of published CyTOF datasets? If so, what do you think would be the best way to collect this information? It could be something as simple as a Google Form....


What is the minimal information that would need to be captured, to make it useful? Obviously, it would be nice to have all the information possible, but that creates a hassle for the generators and becomes a barrier to use.

I was thinking something like this (not all fields required):

Flow Repository ID:
Immport ID:
Other database:
Other database ID:

Organism (human, mouse, etc):
Sample type (eg, PBMC, bone marrow):
Assay type (eg, surface phenotyping, phosphoflow, ICS):
Published (yes/no):
DOI:


Thoughts?

Mike
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jlederer

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Joined: Thu Feb 08, 2018 2:42 pm

Post Mon May 14, 2018 5:41 pm

Re: Useful to have list of CyTOF datasets?

Mike. We should consider immport. They have a lot of this already organized. I think it is a great idea to have datasets available since it helps with analytical development as you pointed out. Also, there are features in datasets that may be of interest that were not the focus of the published works. I would support this initiative. Jim
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mleipold

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Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Mon May 14, 2018 5:50 pm

Re: Useful to have list of CyTOF datasets?

Hi Jim,

Part of why I listed FlowRepository as well is that not every funding agency requires deposition in Immport (especially for non-US datasets). A lot of datasets are being put in FlowRepository upon publication: personally, I find FlowRepository at least a bit less onerous to use than Immport.

I'm only aware of FlowRepository and Immport as currently used databases for CyTOF data, but I added "Other" just in case there are others (now or in the future).


Mike
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mleipold

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Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed Jun 06, 2018 6:21 pm

Re: Useful to have list of CyTOF datasets?

Hi all,

OK, I've set up a Google Form based on my May 14 post to try to capture information about publically available CyTOF datasets.

Form: https://goo.gl/forms/gsCG1ug0pfmmcvaD3
Results: https://docs.google.com/spreadsheets/d/ ... sp=sharing

Please let me know if you have any trouble accessing and filling out the Form, or viewing the Results.


If at all possible, please add your datasets to the list....especially with the backfilling, I can't do it all myself! I made the questions non-required, but the more information collected, the more useful the list will be. :)


Mike
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mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed Jun 20, 2018 3:01 am

Re: Useful to have list of CyTOF datasets?

Hi all,

Just an update: I've noticed that there have been a few additions to the spreadsheet using the form. That's great, but unfortunately, no accession numbers were given in at least 3 instances. For example, on 6/15, someone added a row filling out "Sample type" = "spleen", but no FlowRepository or Immport ID (and no mention of other database).

I've deleted those from the spreadsheet; please re-add them, with associated IDs.


Thanks,
Mike
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mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed Dec 12, 2018 8:53 pm

Re: Useful to have list of CyTOF datasets?

Hi all,

As an update to this thread about CyTOF datasets: I've been adding all the datasets I can find in Immport, FlowRepository, and other sites as I see CyTOF papers published, or as I query the databases directly.

As of today (Dec 12, 2018), there are IDs and links to 154 CyTOF datasets of various sizes, assay types, and organisms (not all annotated to that level of detail). Where applicable, there's a link to the DOI for a paper that used it (in most cases, the first paper that used or generated it).


I would strongly encourage authors to use the Google Form (https://goo.gl/forms/gsCG1ug0pfmmcvaD3) to add their own datasets as they publish papers.


On a side note: I found out recently that Immport only releases updates on approximately quarterly basis. Their next release is currently scheduled for mid-Jan 2019. I have *no* idea why they're so slow in releasing.....


Mike

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