Header Leaderboard Ad


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



No announcement yet.
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.


    Latest Articles


    • seqadmin
      A Brief Overview and Common Challenges in Single-cell Sequencing Analysis
      by seqadmin

      ​​​​​​The introduction of single-cell sequencing has advanced the ability to study cell-to-cell heterogeneity. Its use has improved our understanding of somatic mutations1, cell lineages2, cellular diversity and regulation3, and development in multicellular organisms4. Single-cell sequencing encompasses hundreds of techniques with different approaches to studying the genomes, transcriptomes, epigenomes, and other omics of individual cells. The analysis of single-cell sequencing data i...

      01-24-2023, 01:19 PM
    • seqadmin
      Introduction to Single-Cell Sequencing
      by seqadmin
      Single-cell sequencing is a technique used to investigate the genome, transcriptome, epigenome, and other omics of individual cells using high-throughput sequencing. This technology has provided many scientific breakthroughs and continues to be applied across many fields, including microbiology, oncology, immunology, neurobiology, precision medicine, and stem cell research.

      The advancement of single-cell sequencing began in 2009 when Tang et al. investigated the single-cell transcriptomes
      01-09-2023, 03:10 PM