Specifically, I am wondering if I can predict the surface marker expression of CD14 and CD16 on monocytes based on scRNAseq data that includes the expression level of those two genes. Does anyone have any insight?
Hi Anna Farrell-Sherman
It depends a little bit on the context of your experiment, i.e. sometimes surface marker expression correlates perfectly with transcriptomics data and sometimes it doesn't.
If you have serum or plasma from your samples available run a proteomics experiment assessing expression of your macrophage markers with Olink's PEA platform. CD14 and CD16 are both part of the library as per:
https://olink.com/products-services/biomarker-search/
And on top of that you can run your samples at ISB in Seattle
https://isbscience.org/olink-services/
The protein expression data in circulation is a better surrogate for surface expression on PBMCs as you directly look at the same targets that are shedding into the serum/ plasma fraction.
All the best and good luck with your experiments,
Michael
Thanks Michael! That is very helpful. We actually already have Olink data from these samples. Could you point me to the names of the markers that are in the Olink marker set? When I search for CD16 (or the uniprot number Q9ULV2) nothing comes up.
Hi Anna Farrell-Sherman
I quickly checked the library and found that we cover the following proteins uniprot: O75015 (FCG3B, 233 aa), but not P08637 (FCG3A, 254 aa) or Q9ULV2 (which is a 85 aa splice isoform of FCG3B, if I am not mistaken). For CD14 we cover P08571 (375 aa).
They are all part of the Explore library, whereas O75015 is also included in the Target 96 CVM panel.
Let me know, if that helps or shoot me an email at [email protected]
All the best & good luck,
Michael
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Peptides