Identifying rosa locus expression in snRNA-seq

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2.1 years ago

rbronste ▴ 420

Hi, I am analyzing some snRNA-seq data from sorted cells which were obtained from mice that express two different color reporters via the Rosa locus. I was hoping to be able to check UMAP clusters for expression of these two reporters and not quite sure of how to go about it. If anyone has suggestions that would be great, thanks.

rosa locus snRNA-seq reporter scRNA-seq • 611 views

ADD COMMENT • link 2.0 years ago by rbronste ▴ 420

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Were the transgenes part of the reference you aligned/quantified against?

ADD REPLY • link 2.1 years ago by ATpoint 81k

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Its H2B-GFP expressed from the Rosa26 locus in this particular mouse line so probably not. Its 10X snRNA-seq data, so I guess I would have to go back and realign to Rosa26 that contains the transgene but I was hoping to integrate it somehow into the current alignment if possible, to maintain clustering. Basically trying to identify cells of origin for the reporter in the clustering, to see how leaky it is relative to what we expect.