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Complementary CyTOF + scRNAseq papers

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billog

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Joined: Wed Sep 17, 2014 10:53 pm

Post Mon Sep 17, 2018 3:38 pm

Complementary CyTOF + scRNAseq papers

Hello,

I'm trying to make the pitch that high dimensional cytometry is a good complement for scRNAseq studies and was looking to crowdsource my literature search for any papers in which both technologies were leveraged (low bar) and meaningful biological insights were obtained (high bar) Evan Newell & Florent Ginhoux have a nice publication along these lines and I am looking for help from the forum in finding more...

The paper Mike posted recently doesn't help too much as its more of a comparison than showing any complementary value...

Thx, - Bill
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mleipold

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Location: Stanford HIMC, CA, USA

Post Mon Sep 17, 2018 3:43 pm

Re: Complementary CyTOF + scRNAseq papers

Hi Bill,

Wre you referring to this one? https://doi.org/10.1101/416750


I've recently been looking at scRNAseq + CyTOF papers for another reason. Here are some of the ones I've found.....maybe some of them will be useful?

https://doi.org/10.1371/journal.pone.0179385
https://doi.org/10.1101/116061
https://doi.org/10.1101/395947


Mike
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mleipold

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Post Mon Sep 17, 2018 3:48 pm

Re: Complementary CyTOF + scRNAseq papers

Here's another one: doi: 10.1016/j.jaci.2016.12.971
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billog

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Joined: Wed Sep 17, 2014 10:53 pm

Post Mon Sep 17, 2018 6:28 pm

Re: Complementary CyTOF + scRNAseq papers

Yes, that paper (https://doi.org/10.1101/416750) looks very well done and of high quality but is more about comparing single cell RNAseq with cytometry and not so much about how the approaches can complement each other... link to Ginhoux paper I referenced before is below to give a sense of what I think best fits...


http://dx.doi.org/10.1126/science.aag3009
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AJFilby

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Joined: Wed Jul 22, 2015 2:53 pm

Post Tue Sep 18, 2018 6:41 am

Re: Complementary CyTOF + scRNAseq papers

Hi Bill

Personally I would cast the net wider than just Cytof and look at the synergies between scRNAseq and all other forms of cytometry. No matter what the genomics people say..scRNAseq is cytometry it just has a genomic analytical end point. With the release of totalSEQ and Abseq I think that message will only get clearer.

I think of scRNA as the tech now with the highest possible number of parameters per cell and thus, in Rumsfeld terms, gives us the biggest chance of an unknown unknown or at least a known unknown. We may still get these by lower dimensional approaches such as cytof or fluorescence flow but in many ways these are now our validation technologies. Not least because we can show protein backs up mRNA (hopefully) and look at cellular functionality by cell sorting. A cluster is just a cluster to me until the function has been proven.

So with this all in mind, this paper stands out as a great example of how these technologies work together to discover and importantly validate new cell types through a multi-pronged cytometry-driven approach.

http://science.sciencemag.org/content/356/6335/eaah4573

Kind regards

Andy
Newcastle University FCCF director
ISAC council member for method and technology development
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vtosevski

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Location: Zurich, Switzerland

Post Mon Sep 24, 2018 11:30 am

Re: Complementary CyTOF + scRNAseq papers

Hi Bill,

How about this preprint?

http://biorxiv.org/lookup/doi/10.1101/351130

I cannot judge the limits of statistical validity of what has been done there, but for sure looks interesting.

Vinko

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