Hello All,

We hope to collect some data from specially tagged mouse cells with lacZ. Other than the fact that they are tagged with lacZ, they don't have a distinct marker profile, by which these cells can be recognized.

So, my question is- If we do single cell on these samples, how can we recognize lacZ expressing cells (after mapping to the mouse genome?) Is it even possible?

Or if it isn't, is there a different tagging strategy we need to use to allow us to do a single cell study?

Any comments, suggestions, or pointers to literature, will be greatly appreciated

Thanks, Kavi

Usually this is handled by creating a transgenic genome reference of, e.g., GRCm38 + lacZ, quantifying expression as usual, and then doing whatever downstream analysis you want on the lacZ-positive subpopulation.

Creation of custom references should be straightforward with all major pipelines for scRNA-seq sequence processing.