Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bioanalyser traces + QC postPCR. ChIPseq Illumina protocol

    Hi everyone.
    I have been trying to get ChIPseq libraries. I started with 10ng as suggested by Illumina and got a Bioanalyser trace. Problems: the trace is actually two quite-fused peaks. The first at around 165bp and the second at around 224bp (I cut the gel from 125-150bp to 300bp).
    Is this normal?
    Another question would be if anyone does a QC after the protocol's PCR. imagine you start with the INPUT sample (pre-immunoprecipitated DNA. Your ChIP background control, basically) which is normal fragmented genomic DNA. Before library preparation, you have the same amount for all genomic locations (as seen on RT-PCR). But after library PCR, there is a quite strong bias for some regions compared to others. Is this normal? do you do this QC step or go direcly into sequencing if the library looks fine on the Bioanalyser?
    Cheers everyone in advance!

  • #2
    Did you try to run the IP-ed material (on the Bioanalyzer) before sample prep.? This may give you a clue if the size distribution looked like this before adding the adapters.
    Sorry, not the complete solution, but maybe it give a hint...

    Comment

    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
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    9 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    50 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X