Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bacterial signal in metatranscriptome data

    Hi all. I have some RNA-Seq data from the sequencing of a green algae in co- culture with a bacterium. The bacterial cell numbers were reported to be in a 50:1 ratio with the green algae. However, only ~7% of the reads are ascribed to bacteria, the rest are algae/ plant. I have argued myself silly around this matter but this seems a low ratio of bacterial to algal signal but I can think of no way of knowing. Ultimately the aim is to publish a comparison of functional activity amongst based on metatranscriptomic reads from both algae and bacteria. I'm concerned about what would be an expected (publishable) signal from the bacterial population for this kind of study.

  • #2
    How was the RNA prepared?

    Comment


    • #3
      Total RNA was prepared by grinding a frozen pellet followed by the Ambion ToTALLY RNA kit. cDNA libraries were prepared after double depletion of rRNA using the plant, then bacterial RiboZero kits.
      Last edited by chc*; 05-25-2016, 11:13 PM.

      Comment


      • #4
        I wouldn't expect the cells to lyse at exactly the same rates. Also, algal genomes are far bigger than bacterial genomes, and the cells are bigger as well. So I would expect plant reads to be much more abundant than the cell count ratio would suggest. Maybe you could find out the expected amount of RNA in a plant vs bacterial cell and see if that makes the math work out?

        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
        11 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        51 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        68 views
        0 likes
        Last Post seqadmin  
        Working...
        X