Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • universal 18s eukaryotic primers

    I'm wondering if anyone has identified a good primer pair that spans the 18s rRNA v4 region and is proven to work well on the MiSeq platform. I haven't found any established protocols in the literature yet. Most of the recent publications from 2014 refer to 454 sequencing. I'd be interested in other primer suggestions spanning v5, v7 and v8 as well. I've found this paper useful, "Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers" by Hadziavdic et al., but again, all these primers were designed with 454 in mind.

    If anyone is willing to share universal eukaryotic 18s primers and amplification protocols they have found to work well on the MiSeq, I'd be really appreciative.

  • #2
    Don't know if this helps, but take a look here:

    Comment


    • #3
      The biggest concern for 18S (even more so than 16S) is to get complete overlap of forward and reverse since most people looking at Euk SSU are wanting to talk about single base changes. Without complete overlap, your quality won't be high enough to consider single bases. So look at the available primers and choose a few sets that seem to be roughly 250-300bp long (miseq v2 500 cycle or v3 600 cycle). Do some in silico pcr against a big database like Silva and see if the "universal" primers are universal enough for your groups or if they are biased against things that you are interested in.
      Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.

      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