About inconsistent cell counts per samples obtained in small nuclear RNAseq data.

Question

[bk11]

Hi,

I have single cell small nuclear RNAseq data with inconsistent number of nuclei detected per samples ranging from 250 to 18100 with average count being 5220. So, my question is how we can process these data to get meaningful results. [NOTE: The Average Expected Recovery of Nuclei for each sample was ~7200].

Any suggestion or help will be appreciated.

[rpolicastro]

Do you mean single nucleus RNA-seq?

Whether you can perform a particular type of analysis will depend on a few factors such as how many cells of interest you capture and your experimental group compositions. You're better off asking specific questions about specific analysis you want to perform and providing as much relevant info as possible.

[bk11]

Yes. These are the single nucleus RNA-seq data. We expected to have ~7000 nuclei but unfortunately majority of samples have nuclei counts either very low or higher than expected counts. We have both disease and healthy control samples in these datasets. The idea is to identify single cell populations in the tissue of our interest and find differentially expressed genes in each single cell types we can identify in diseased samples compared to healthy controls.