Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Small RNA library: 30nt peak?

    I performed an RNA-seq experiment and observed an unusual size distribution of small RNAs (image attached). I was wondering if anyone has seen this before.

    I used Ambion's mirVana small RNA kit to extract and enrich for the sRNA fraction (<200nt). Used the Ion Total RNA-seq kit v2 to create libraries, and the Ion Proton platform for sequencing. In addition to the 21-24 nt peak corresponding to miRNA and siRNA, my libraries include a ton of ~30 nt reads after mapping to my genome.

    I tried Rfam and some tRNA databases, but didn't have any luck annotating them. When I BLASTed the most abundant 30nt reads at NCBI, it returned protein-coding genes from various organisms. My RNA prep was clean, with no significant degradation. The peak is broad but well-defined, dropping off around 36nt.

    Could these mystery reads be some kind of noncoding RNA that I simply haven't heard of? Are you familiar with this type of length distribution?
    Attached Files

  • #2
    .........piRNAs?

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Genetic Variation in Immunogenetics and Antibody Diversity
      by seqadmin



      The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
      11-06-2024, 07:24 PM
    • seqadmin
      Choosing Between NGS and qPCR
      by seqadmin



      Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
      10-18-2024, 07:11 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 11-01-2024, 06:09 AM
    0 responses
    29 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-30-2024, 05:31 AM
    0 responses
    21 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-24-2024, 06:58 AM
    0 responses
    26 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-23-2024, 08:43 AM
    0 responses
    57 views
    0 likes
    Last Post seqadmin  
    Working...
    X