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2016-Catena et al-Cytometry A

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mleipold

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Post Thu Mar 31, 2016 8:45 pm

2016-Catena et al-Cytometry A

"Enhanced multiplexing in mass cytometry using osmium and ruthenium tetroxide species"
Catena, R., Özcan, A., Zivanovic, N. and Bodenmiller, B.
Cytometry A, 2016
http://dx.doi.org/10.1002/cyto.a.22848

-use of OsO4 and RuO4 for barcoding
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tjchen

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Joined: Wed Nov 20, 2013 11:43 pm

Post Tue Apr 12, 2016 8:54 pm

Re: 2016-Catena et al-Cytometry A

If you are interested in accessing the raw data, Raul made the supporting data publicly available.
http://www.cytobank.org/bodenmillerlab (clicking on the paper title should take you to the Cytobank project)

I also want to make a small PSA for making data publicly available post-publication and even preparing a link to the data during journal submission. There are a few options for doing this--feel free to ping me if you have questions about how to set it up (with or even without Cytobank).

Fundamentally, making the data publicly available helps with scientific transparency and retrospective data analysis and collaboration, and I encourage everyone to do so if possible.

Cheers,
~TJC
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mleipold

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Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed Apr 13, 2016 3:10 pm

Re: 2016-Catena et al-Cytometry A

Hi Tiffany,

Due to grant reporting requirements, I know that an increasing number of people are publishing their data sets on ImmPort. For example, access number SDY232 from Strauss-Albee et al 2014 (http://dx.doi.org/10.4049/jimmunol.1401821).

I also know that ImmPort's search function isn't the best: I've had trouble finding some CyTOF stuff I knew was in there. In some cases, I had to search by investigator, in other cases I had to search by "CyTOF" or "mass cytometry".


Is Cytobank interested in keeping an updated list of CyTOF data sets in ImmPort? It would be great of course if you chose to host a mirror of them, but even having a more reliable link to the accession numbers (or directly to the sets themselves on ImmPort) would be helpful.


Mike
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antonio

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Post Wed Apr 13, 2016 3:33 pm

Re: 2016-Catena et al-Cytometry A

There is also FlowRepository that was originally implemented from Cytobank. At least now it look like the old version of Cytobank. It would be nice to have a common repository.
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AdeebR

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Location: NYC

Post Thu Apr 14, 2016 12:07 am

Re: 2016-Catena et al-Cytometry A

I also strongly support making published cytometry data publicly available, but I think that for this practice to be widely adopted by investigators the process needs to be as streamlined and pain free as possible (or made mandatory by funders or publishers - e.g., Cytometry, which requires that the data be be uploaded and made available to reviewers)

I like FlowRepository as a way of making cytometry data publicly available since it takes fairly little effort and the interface is pretty user friendly (particularly if you're used to Cytobank).

Immport unfortunately has some pretty involved and laborious uploading requirements and while it's true that this probably means that datasets are ultimately well annotated I think this is likely a major barrier for many investigators unless they're obligated to do so due to NIH funding requirements.

For those of us who use Cytobank, it would be easiest to simply designate experiments as "public" on Cytobank and this has the advantage of also allowing an easy share of the associated analyses and visualization. One of the problems there is that for those of us using an institutional version of Cytobank that this only makes the data public on the institutional server and not to the general public Cytobank.

Adeeb
Adeeb Rahman
Icahn School of Medicine at Mount Sinai, NYC
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tjchen

Participant

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Joined: Wed Nov 20, 2013 11:43 pm

Post Thu Apr 14, 2016 5:22 pm

Re: 2016-Catena et al-Cytometry A

All good references in this thread for posting publicly available data -- we've helped people put data on both FlowRepository and Cytobank at the same time and I have enjoyed working with immuneXpresso http://www.immport-labs.org/immport-immunexpresso/ . If anyone has any others I would be interested to know as well.

Unfortunately since there is no one-size-fits-all solution currently, so cross referencing the data (for us, it's posting a Cytobank project link) is the most common answer to putting the same data across multiple repositories, although it is not ideal. Right now we haven't moved data without the authors doing it themselves, but consolidating data that is already publicly available is very valuable/useful. I think this is probably out the scope of an email discussion.

To address Adeeb's question, there is also a way to move your whole Cytobank experiment to give to the community. Premium Cytobank lets you give your SPADE and viSNE analyses to the world, but it is a subscription-based server (although you can log in with an expired account--it limits access to tools). The steps for moving an experiment are (1) export the entire ACS from your enterprise Cytobank, (2) upload it to the premium server. Right now, for data and gating analysis alone, we disseminate most of these ACS-transferred datasets onto Community Cytobank for simplicity.

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