Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • 127bp adaptor dimer

    Hi all,

    I ran Bioanalyser on the PCR products of my RNA-Seq library prep, and there are adaptor dimers contamination in all my samples. Some are more serious (sample 1) than the others (sample 3) as the starting amount of RNA varies among my samples. Pls see attached pic.

    Should I do a AMPure beads purification on all? Or should I do a gel purification instead? Do all my samples (sample 1,2 and 3) all warrant 2nd purification in order to get rid of the adaptor dimers? I am going to run a multi-plex Hi-Seq run, 8-12 samples per lane, so it will be ~25M per sample.

    Thanks a lot!
    Attached Files

  • #2
    Hi Chipgal,
    We use long fusion primers in our workflows and they can be tough to get rid of. As a first option I would try ampure clean-ups - I suspect an ampure ratio of 1.2 might do the trick.... it does depend on input DNA and a few other factors so you could titrate. There are some threads on this if you search... for example check out http://www.keatslab.org/blog/pcrpuri...mpureandsimple

    Cheers, Mike

    Comment


    • #3
      Hi Chipgal,

      We see the adapter dimers sometimes. Usually do 1X AMPure beads purification to get rid of the dimers, as it affects the number of sequencing reads a lot.

      Thanks,
      Wei

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      66 views
      0 likes
      Last Post seqadmin  
      Working...
      X