Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • mRNA-seq illumina GAII - microRNAs?

    Hi,
    I have a question about finding pre-miRNAs precursor sequences among dataset from mRNA-seq? Is it possible since it is polyA method or the protocol preparation is somehow filtering only protein-coding long transcripts and it is highly unlikly to find miRNA precursors/transcripts among mRNA-seq data?

    Thanks
    ------------
    SMART - bioinfo.uni-plovdiv.bg

  • #2
    up

    same question but with a TruSeq small RNA library kit and 36nt long reads.

    Comment


    • #3
      We definitely see pre-miRNA in our RNA-seq data sets. We use the TruSeq RNA kit which of course does a polyA pull down. We align to RefSeq and there are about 760 mirs in the mouse database. They are denoted with NR_xxxxxxx IDs. With the small RNA library prep I don't see them because I do a small RNA isolation step prior to library production which will get rid of the pre-mirs. I would assume that if you generated small RNA libraries on total RNA then you might get them based on which peaks you end up recovering after library amplification.

      Comment


      • #4
        Thanks brooksma,

        Do you know some papers talking about RNA-seq and pri-miRNA detection ?

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Exploring the Dynamics of the Tumor Microenvironment
          by seqadmin




          The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
          07-08-2024, 03:19 PM
        • seqadmin
          Exploring Human Diversity Through Large-Scale Omics
          by seqadmin


          In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
          06-25-2024, 06:43 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 07-10-2024, 07:30 AM
        0 responses
        25 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-03-2024, 09:45 AM
        0 responses
        201 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-03-2024, 08:54 AM
        0 responses
        211 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-02-2024, 03:00 PM
        0 responses
        193 views
        0 likes
        Last Post seqadmin  
        Working...
        X