Mutational analysis on 10X scRNA-seq 3' v3 library
Hello, I have a 10X scRNA-seq 3' v3 library. I would now like to assess whether certain cells in the dataset harbor a known mutant variant - a short 3' deletion in the coding region of our gene of interest. I'd like to PCR amplify the gene of interest using an aliquot of the 10x library and then directly sequence. Any advice on how to design primers that would capture the 3' mutation as well as the cell barcode (in order that I could determine whether individual cells have the mutant variant or not). All input would be greatly appreciated. Thank you! Kevin
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Kevin.OConnor •
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Sounds like you want to use a technique similar to Genotyping of Transcriptomes or what the authors of this paper did. You may want to reach out to those authors directly.
Thank you so much. Will do!
You may want to post this over at SeqAnswers.com or Biology stackexchange. It would be more appropriate for those forums.
Thank you- I will post over there as well. Appreciate your suggestion.