Library preparation for single cells RNA sequencing ends being the most expensive part of the of the process, so it's way cheaper doubling the reads depth than the number of samples. I have seed already somebody pooling mouse and human cells in the same sample and then demultiplex the cells by using unique transcripts to reduce the costs of scRNAseq. Also, I just ended up reading of the so-called CROP sequencing in which you use the sgRNA transcript to demultiplex multiple cells with different sgRNA vectors.

I wish to single cell sequence a pooled sample of WT cells and CRISPR KOs and demultiplex them later. Unfortunately, the expression of my target gene is not sky high so it's likely I'll have lots of dropouts for that mRNA and I cannot use the CAS9 induced InDels to distinguish WT from KOs. Also, the plasmid I used was not designed for CROP seq so I don't have any reporter sgRNA with a poly A tail. I was thinking instead of using the puromycin resistance cassette to separate the KOs from the WT since it should be stably expressed by the EF-1α promoter.

Does anyone have any experience or comments on that practice?