Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • SamCurt
    replied
    I agree with pmiguel; this is typical of TRIzol extractions. Because I usually think DNAse treatment should remove all of the gDNA in the sample if used as directed, I won't worry much about gDNA contamination.

    Of course pasing through a column would remove this peak, but this can also be done by isopropanol precipitation using a lower volume of isopropanol relative to the aqueous phase.

    Leave a comment:


  • pmiguel
    replied
    Sure, they could be DNA fragments -- but to me this looks like a normal Trizol extracted RNA chromatogram. Overall pico chips are more sensitive than nano chips, obviously. But I have not noticed pico chips being unusually sensitive to shorter molecules.

    Again, if the low molecular weight stuff is really bugging you, just get rid of it.

    --
    Phillip

    Leave a comment:


  • Ken_HK
    replied
    Thx for your answer. But do you think is there any chance that those peaks are DNA fragments? Moreover, I used the RNA 6000 pico kit. Will that be more sensitive to small fragments compare with nano kit and that's why I have a high cluster of peaks below 200nt?

    Leave a comment:


  • pmiguel
    replied
    Originally posted by Ken_HK View Post
    Hi, I have a RNA sample from Trizol RNA extraction with Bioanalyzer QC 28s/18s:1.8 and RIN 9.4. However, there is a high peak below 200nt. Can I use this sample for RNA-seq? Pls also see the attached RNA profile
    Sure, your RNA looks great. Trizol preps normally do not remove the small RNAs abundant in all cells. That is what you are seeing below 200 nt.

    The only caveat I can think of is that if you are doing standard RNAseq, input amounts of RNA may not be calibrated for large percentages of the total RNA prep being small RNAs. It should not present a problem in your case, but I have seen preps where it looked like >70% of the RNA was small.

    If you are concern there are lots of methods to fractionate away the small RNAs. For example Zymo RNA clean up columns come with a method for washing off small RNA prior to eluting.

    --
    Phillip

    Leave a comment:


  • Ken_HK
    started a topic Can I use this RNA smaple for RNA-seq

    Can I use this RNA smaple for RNA-seq

    Hi, I have a RNA sample from Trizol RNA extraction with Bioanalyzer QC 28s/18s:1.8 and RIN 9.4. However, there is a high peak below 200nt. Can I use this sample for RNA-seq? Pls also see the attached RNA profile
    Attached Files
    Last edited by Ken_HK; 12-22-2011, 01:21 AM.

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
52 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X