In the cytof table I can find cell type frequences for the following cell types:
Are plasmablasts missing? I still am not quite familiar with the different immune cell markers but on the Bio-Rad website (B Cells Overview (from Discovery to Therapy) - Mini-review | Bio-Rad) I found a table which lists biomarkers for plasma blasts as CD20-, CD38 high, CD27 high, CD183+ and others but I don’t see any of these markers within the list of cells from above. Should we use just B-cells for this task?
Hi @joreyna you are making really good points and this is obviously an issue that we should resolve.
Plasmablasts in our data were obtained manually. I am not sure if your list has them missing due to the fact that they were manually gated while the ones you are listing were obtained by automated gating.
In our case, the plasmablasts were obtained by first gating at “B cells” based on CD19 expression, then we used a dot plot to select CD20- CD38+ cells. Those ones were named plasmablasts or ASCs (Antigen Secreting cells).
So thanks again for your work on this. This really helps us identify the issues with the data.
@Pramod, why do you think might be the issue? The fact that we have a different table for the plasmablasts? The automated vs manual gating?
So the database currently has a CyTOF (cytof) table and Cell Info (cell_type) table which we can merge using the cell name. I did that and I generated this table:
Seems like there is some extra white space for NK and mDC cells. For plasma cells, I could only find them in the Cell Info and I also see they are the only manually gated ones (in red). What does it mean for cells that don’t have a gating method like Basophils?
Thanks @joreyna for letting us know about various issues in CyTOF table.
Following issues are fixed now:
Thanks for the update Pramod!
