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10x 5' GEX - overrepresentation of RT Primer in results

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  • 10x 5' GEX - overrepresentation of RT Primer in results

    Hi all -

    First time post so apologies if this is the wrong spot..!

    I'm having issues with my first 10x 5' gene expression run and am looking for help troubleshooting what went wrong.

    The sequencing resulted in a low percentage of reads mapping to the transcriptome (~30%). Further investigation revealed an over-expression of RT Primer in Read 2. Read 1 appeared fine.

    We loaded 8000 cells and detected 6000-9000 cells (in 4 samples). Knee-plots looked good, with not much background or degraded RNA. Bioanalyzer traces taken after cDNA amplification and after library completion both looked ok.

    Samples were PBMCs treated for 18 hours with exosomes.

  • #2
    Hi @egotistdown, I am wondering whether you figured out the reason. I encountered the same issue. Thanks.

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