Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • technical replicates uncorrelate with each other

    Hi:

    I do chip-seq aganist gammaH2AX, one of histone modification, which indicates DNA damage and repair.
    At the beginning I just have about 7M reads (chip) and 4.7M reads (input) and using SICER to get enrishment profile on genome (human hg18).
    Then I send the exactly the same sample to sequencing (chip sample) and getting 11M reads and I don`t sequence input sample this time and use the same input to get enrishment profile.
    My question is I find those two profiles have large differences.

    can you give me some advice?
    thanks in advance

  • #2
    Hi
    - did you confirm the SICER peaks by qPCR on unprocessed ChIP samples or any other technology?
    - are there positive/negative regions already documented and do your sequencing results conform to those?
    - my initial guess is that you a) do not have enough reads for a robust analysis b) differences in sequencing depth will be the main source for inconsistency. c) most of your SICER peaks are false positives

    Comment


    • #3
      thanks mudshark

      1. I have ordered primers to do the verification via qPCR
      2. what do you mean by positive/negative regative?
      3. I hope the variability occurs just beacuse I don`t have enough reads.

      Comment


      • #4
        When you say you sequenced exactly the same sample does that mean that you:
        1) Made a new library from the same ChIP or
        2) Made a single library from one ChIP and sequenced it twice?
        --------------
        Ethan

        Comment


        • #5
          Thanks ETHANol

          The exactly the same sample means just one library and I sequence it twice

          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, 03-27-2024, 06:37 PM
          0 responses
          12 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-27-2024, 06:07 PM
          0 responses
          11 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          53 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          69 views
          0 likes
          Last Post seqadmin  
          Working...
          X