Header Leaderboard Ad

Collapse

noncoding RNA

Collapse

Announcement

Collapse

SEQanswers June Challenge Has Begun!

The competition has begun! We're giving away a $50 Amazon gift card to the member who answers the most questions on our site during the month. We want to encourage our community members to share their knowledge and help each other out by answering questions related to sequencing technologies, genomics, and bioinformatics. The competition is open to all members of the site, and the winner will be announced at the beginning of July. Best of luck!

For a list of the official rules, visit (https://www.seqanswers.com/forum/sit...wledge-and-win)
See more
See less
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • noncoding RNA

    What is the best practise for detection of novel long noncoding RNA as well as the expression of known lincRNA. A litertaure survey showed Ribo depleted, Ribo zero, Hexamer approaches. I wonder if there is a study comparing existing methods of isloating non coding RNA or any best method. It will be great to have feedback if some one has tried varoius methods and their working experience on which approach may be best. Thanks

  • #2
    You can't simply enrich for non-coding RNA. The method people use is to generate two datasets. Total RNA-seq and Ribo-seq. Then, you need to look for regions that are found in the total RNA-seq dataset, but not in Ribo-seq.

    Comment


    • #3
      long noncoding RNA detection and quantification experiment

      Thanks Dario1994,
      Consider me as new in this area and I am getting little confused with the literature available e.g http://mbio.asm.org/content/1/5/e00206-10.full
      suggest that non-ribosomal RNA should give ncRNA? Any thoughts?

      Comment


      • #4
        I understand why you are confused now. The issue is that most lncRNA don't have a poly-A tail, so the older method of enriching for RNA in the sample by grabbing them with oligo dT sequences missed a lot of them. Ribosomes are some of the most common RNA in the cell, and they do not have A-tails. You can avoid most of your sequencing reads originating from them by doing poly-A enriched RNA sequencing.

        The other approach to RNA sequencing is total RNA sequencing. But, the problem with this is that ribosomes are highly present in the sample. So, you need to do the ribosome depletion treatments to get rid of them. But, with this method, you won't lose the lncRNA without the poly-A tail.

        My original point was that by doing RNA sequencing of any kind, you can't simply tell if a new transcript you find in your data is protein-coding, or not.

        Comment


        • #5
          noncoding RNA detction

          I am also looking for the ways to detect noncoding RNA, Waht is teh ebst strategy to detect and quantify noncoding RNA . Papers have described selective use of Ribo depletion to enrich linc RNA. However it has been suggested just depletion of Ribo RNA may not be sufficient to enrich linNoncoding RNA.



          Any suggestion what should be the best way to go - just ribodepleted or both polA vs Ribo-depleted libraries should be best to detect linc noncoding RNA.

          Comment


          • #6
            noncoding RNA

            I have a very basic question is there a rule what may be good for detection of noncoding RNA (long), -PE or SE longer read in case of ribo-depleted. Is there an advantage/ disadvantage of one over the other. Literature search suggest use of SE/ PE both and even longer SE reads. Any thoughts or experience?

            Comment

            Latest Articles

            Collapse

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 06-01-2023, 08:56 PM
            0 responses
            9 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 06-01-2023, 07:33 AM
            0 responses
            9 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 05-31-2023, 07:50 AM
            0 responses
            4 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 05-26-2023, 09:22 AM
            0 responses
            11 views
            0 likes
            Last Post seqadmin  
            Working...
            X