Should I use Integrated or RNA assay for my analysis?

[rfayaz-29]

Hi, I’m analysing scRNA-seq data (samples are tagged for knockout lung/spleen and wild-type lung/spleen and sample tag for CD45). I originally did DEG, GO, and GSEA using the integrated assay and got more than 50 significant DEGs and relevant/expected immune pathways (cytokine signalling, migration, etc.)

After switching to the RNA assay (as recommended), I now get:

only ~29 significant DEGs
GO not really possible
GSEA gives odd terms (e.g. all terms with p.adjust <0.05 are neuronal/synapse related)

Questions:
Is this drop in DEGs expected when switching to RNA?
Were my integrated results likely misleading?
What should I check to make sure my RNA results are correct?
Is RNA assay always required for DEG?

Any insight would be much appreciated.

I'm a beginner at scRNAseq, please forgive my ignorance and thank you for your help!