Mutational analysis on 10X scRNA-seq 3' v3 library

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3.9 years ago

Kevin.OConnor • 0

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

RNA-Seq single cell RNA-seq scRNA-seq • 1.3k views

ADD COMMENT • link 3.9 years ago by Kevin.OConnor • 0

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You may want to post this over at SeqAnswers.com or Biology stackexchange. It would be more appropriate for those forums.

ADD REPLY • link 3.9 years ago by GenoMax 141k

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Thank you- I will post over there as well. Appreciate your suggestion.

ADD REPLY • link 3.9 years ago by Kevin.OConnor • 0

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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.