I have single cell RNA-seq data on about 2000 cells in 9 time point. I have clustered my cells in each time point by Seurat. I am seeing in some time points I have 3 clusters while in another time points I have 2 clusters of cells (please look at the plot).
One hypothesis would be that, a new cell type is being emerged at last time point. But maybe if we had another further time point this third cluster being disappeared because that has been arose just because of undifferentiated cells from the later time point (second hypothesis).
Another hypothesis would be this new third cluster is a new cells type that only temporarily expresses a set of genes but if we had cells for another further time point, we would not see the expression of these genes anymore and we had again 2 clusters. I am really struggling with this how I could test my hypothesises.
The final hypothesis would be that the third cluster is really a new cell type born from old cell types during the differentiation.
Any suggestion would be highly appreciated.