Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • honey
    replied
    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?

    Leave a comment:


  • pattalN
    replied
    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.

    Leave a comment:


  • Dario1984
    replied
    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.

    Leave a comment:


  • mathew
    replied
    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?

    Leave a comment:


  • Dario1984
    replied
    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.

    Leave a comment:


  • mathew
    started a topic noncoding RNA

    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

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, 07-19-2024, 07:20 AM
0 responses
38 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
61 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Working...
X