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Cytof vs. ssRNAseq

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Please be as geeky as possible. Reference, reference, reference.
Also, please note that this is a mixed bag of math-gurus and mathematically challenged, so choose your words wisely :-)
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Osiris

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Posts: 13

Joined: Fri Jul 25, 2014 1:30 pm

Location: Zurich, Switzerland

Post Tue Nov 14, 2017 1:02 pm

Cytof vs. ssRNAseq

Hi there,

Does anyone know of a paper comparing cytof and ssRNAseq in terms of success of cluster identification? For example, determining if the Cytof panel markers faithfully find all the cell populations present in a data set, when compared to a completely "unbiased" approach like ssRNAseq where you would have all the possible parameters available for use in cluster identification/assignment?

Thanks!
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lrolsen

Participant

Posts: 5

Joined: Tue Oct 11, 2016 6:21 am

Post Tue Nov 14, 2017 1:10 pm

Re: Cytof vs. ssRNAseq

Hi Dunja,

Not a direct comparison, but the CITEseq authors did some clustering using both scRNAseq and CyTOF and showed that they did better if including both data types rather than one or the other.

https://www.nature.com/articles/nmeth.4380

Best,
Lars
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mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Tue Nov 14, 2017 4:52 pm

Re: Cytof vs. ssRNAseq

Hi Lars and Dunja,

Lars: I only see fluorescence flow experimental info in the Methods in that Nat. Methods paper.....though your point stands.


Dunja: There's also the PLAYR paper (http://dx.doi.org/10.1038/nmeth.3742), which does CyTOF using both protein and RNA targets.

One great thing about the PLAYR paper is that the researchers (to their credit) demonstrate that RNA and protein levels aren't always correlated (eg, Figure 3E, ITGAX).

This was also seen with MET in this paper (https://doi.org/10.1186/s13059-016-1045-6), which used anti-protein antibodies with primer tags for proximity extension readouts along with the RNA (see Fig 3 and following discussion) Also, this paper (doi: 10.1038/s41598-017-03057-5) had some other cases of good or poor correlation between mRNA and protein levels.

Therefore, I think you have to be careful about the idea that scRNASeq and protein-based CyTOF *have* to agree, or that if they don't, one is "wrong". There's a vast amount of literature on transcriptional regulation vs translational regulation, how many proteins a given RNA molecule makes (and the occasional long-tail outliers), and the relative rates of degradation of the RNA and the protein it codes for (I'm a protein biochemist by training, so I'm a bit biased :) .


Mike
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lrolsen

Participant

Posts: 5

Joined: Tue Oct 11, 2016 6:21 am

Post Tue Nov 14, 2017 6:27 pm

Re: Cytof vs. ssRNAseq

Ah, my bad. I think Rahul Satija presented some CyTOF/scRNAseq co-analysis data at the Keystone conference in Stockholm in May. Might be worth contacting him if you need further information on the topic.
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Osiris

Participant

Posts: 13

Joined: Fri Jul 25, 2014 1:30 pm

Location: Zurich, Switzerland

Post Wed Nov 15, 2017 8:53 am

Re: Cytof vs. ssRNAseq

Thanks a lot for the info and references!

Best,
Dunja

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