Question: Identifying a human transgene in mouse scRNAseq data
0
gravatar for ian.folkert
11 weeks ago by
ian.folkert0 wrote:

Hi everyone,

I apologize if there is a simple answer to this out there. I'm working with a scRNAseq dataset of mouse tumor cells that are driven by the expression of a translocation product made from the human tumor cDNA sequence. When I search for either of the single genes that make up the translocation product in Seurat, I don't seem to be able to reliably identify them. I was wondering if anyone has any experience or ideas on the best way to look for this translocation product in the scRNAseq data so that I can confirm which cells are expressing this gene. Thanks so much for the help,

-Ian

rna-seq scrna-seq • 105 views
ADD COMMENTlink modified 11 weeks ago by genomax85k • written 11 weeks ago by ian.folkert0

How similar was this transgene to mouse? If it was similar/identical then unless it had some internal marker it would be difficult/impossible to identify it. I am just thinking out aloud.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by genomax85k

10x? Dropseq? Details please. ALso about the gene. Is it just the cDNA that is expressed? If it is e.g. 10x-based scRNA-seq with 3' enrichment then check if the 3' end of the interesting gene is unique enough to find it. Is it maybe orthologous to other genes in mouse? Then you could not reliable identify it. Maybe the 3' part is multimapping, then it would inherently difficult to detect it if you used alignment-based quantification.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by ATpoint36k
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