I've run an experiment where I collected orans from 3x healthy control mice, and 3x post-injury mice - and ended up generating around 3000 individual single cells from each sample. For consistency and cost reasons, we pooled our 3x single cell sorts together into 2 lanes of the same 10X chip - so generated 2 samples (but each derived from 3 original mice).
Does this represent a publication-quality dataset by 2022 standards?
And (hoping that it does) - is it valid to use these datasets to identify any novel cell types which are gained/lost in the injured organ?
Finally - what would the best tests be to identify the different populations? and would it be essential to confirm this in a second RNAseq dataset? and would it also be essential/preferable to provide additional biological verification using completely separate approaches - e.g ISH, antibody-co-staining etc..
Any tips would be hugely helpful!