Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • microRNAs in RNA-seq?

    Hi,

    I'm sure my question is a really common one, and although I could find a few different opinions on this topic I would like to ask it anyway, just to get a definite answer.
    Is it possible to identify differentially expressed microRNAs in a normal RNA-seq experiment (i.e.not small RNA-seq)?
    We're considering to do a miRNA microarray but will definitely do a RNA-seq in the near future, i.e.were wondering if we don't have to do the microarray at all.

    Thanks,
    Jeannine

  • #2
    Hi,

    You can use the RNA-Seq libraries for identifiyig differentially expressed full pre-miRNA or partly degraded pre-miRNAs which generally include mature miRNAs. First of all, you blast the all desired pre-miRNAs against the RNA -Seq libraries (for good result, not map the contig sequences, directly mapping to unigen sequences).Then, you sort out the outputs for getting the pre-miRNAs and check the expression level of obtained sequences.

    Comment


    • #3
      Hi,

      I am not sure if anybody has shown that the expression of pre-miRNAs is a good substitute estimate for mature miRNAs, at least this article indicates the contrary: http://nar.oxfordjournals.org/lookup...ll&uritype=cgi .
      In any case, with "normal" RNA-seq you will definitely not see any mature miRNAs that require specific shortRNA prorocols to capture and sequence the short sequences.

      Cheers, Hilmar

      Comment


      • #4
        Deli is right. Just wanna add that very few pri-miRNAs will be detected in the transcriptome (my rough guess based on experience is probably 10% of the total miRNA families). Why not do a small RNA-seq instead of miRNA microarray?
        Last edited by Melissa; 09-28-2012, 12:06 AM. Reason: Sorry i mean pri-miRNA instead of pre-miRNA. Still get confused sometimes.

        Comment


        • #5
          and pre-miRNA are not poly-A (pri-miR are) so you've to do ribo depletion libs.
          and like Melissa said: try small RNA-seq instead

          Comment


          • #6
            you definitively would not see miRNA in your RNA-seq data

            Comment


            • #7
              Could any one point me to the best annotation file to count over annotated mature miRNA sequences? I am currently using the gff file off of mirbase (is this reliable?).

              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,...
                Today, 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
              24 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
              25 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 10-23-2024, 08:43 AM
              0 responses
              56 views
              0 likes
              Last Post seqadmin  
              Working...
              X