Congratulations Dr. Rahul Ragunathan on a successful defense @fanglab.org 🎉🎉

We think this artifact may be more pronounced in single cell proteomics as compared to transcriptomics as proteins are a considerably smaller than the transcript that encodes them

We applied this classifier to human cancer cell lines (that I had previously prepared and without excluding cytox green positive cells) and identified permeable cells with a highly correlated proteomic signature to the primary mouse cells.

We found that this leaking signature was similar between different cell types, and thus found it appropriate to train a classifier for the detection of permeabilized cells for sample preps where cytox green was not or could not be used.

These differences were clearly visible in a umap projection where cells partially clustered by permeability status

When we compared the proteomes of permeable to intact cells within a cell type, we noticed a preferential loss of proteins from specific compartments (most prominently, the cytoplasm)

We find that when cell suspensions were frozen down, the fraction of permeable cells increased for all cell types, but disproportionally affected certain cell types

Congrats! @pierresabatier.bsky.social Finding from figure 7C that long lived proteins have lower abundance in dividing cells is indeed striking!

Our paper on dilution due to cell division impacting abundance in a deg rate dependent manner explains this phenomenon. www.biorxiv.org/content/10.1...

Got this wonderful anniversary gift from SO today ❤️

When comparing growing and non-growing cells, the difference in clearance rates is more substantial for long lived proteins, and thus their abundance is reduced in the growing state unless synthesis rates compensate. We find this compensation is insufficient to explain these changes.

However, in growing cells, protein dilution dominates degradation and this influence is lost. Thus in growing cells, less variation is explained by degradation as past work has established.

In cells that are not growing, this influence can control up to 50% of the variation in protein levels.

Oh wow, 10X and ultima think its a good idea to do more mRNA seq on 1 billion cells?? Shocking, unexpected

Had so much fun visiting Max Delbruck in Berlin talking science and doing some nPOPing! If in Europe and interested in getting started with multiplexed single cell sample prep on the cellenONE, finally a good time to reach out!