What counts as a valid biological replicate in single cell RNAseq?

Forum:What counts as a valid biological replicate in single cell RNAseq?

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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!


statistics


biological


replicates


scRNA-seq

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