Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Availability of RNA-seq technical replicates

    Hi all,

    I'm looking for RNA-seq datasets (from any of the popular short-read platforms) that contains more than two technical replicates per sample. I specifically need read counts, not normalized data, also preferably poly-A enriched RNA but I could use anything, and any organism will do. I can find plenty of read count data from duplicate technical replicates, but I'm looking for data with at least 3, but preferably as large number of technical replicates as possible. I wonder if anyone really dug into the reproducibility or RNA-seq in their hands and did 10 technical replicates from a given sample? Sorry, RNA-seq beginner here and don't know the field that well, so any and alll replies will be helpful.

    Thank you!
    -yumpe

  • #2
    No one does technical replicates since they don't add any value to the datasets. Are you looking for "biological" replicates?

    Comment


    • #3
      As it said in my original post, I'm looking for "technical" replicates.
      Maybe I am one of the few people interested in the technical variability of a technique.
      Still am, and grateful for any pointers.
      Thanks!
      Last edited by yumpe; 09-15-2020, 12:58 PM.
      -yumpe

      Comment


      • #4
        You will need to look around to find such data. A library run on multiple lanes (which would be technical replicates) may just be concatenated into a single file for analysis and may not be reported specifically in papers.

        I found this paper (which is not for RNAseq) but does contain technical replicates.

        Comment


        • #5
          Thanks GenoMax, appreciate your help.
          I'm specifically looking for RNA-seq data.
          I'll keep looking!
          -yumpe

          Comment


          • #6
            You might try to look at some of the method/kit comparison papers, or a paper describing a new library prep method. They often compare inter and intra assay performance of replicate inputs, usually Universal Human Reference RNA.

            You'll likely only find older papers using technical replicates. The outcome of the early characterization experiments was that technical replicates are unnecessary, especially in comparison to the added value of biological replicates. They're essentially an elaborate way to burn money, but I'm sure Illumina would love you if you find an argument for them...

            Comment


            • #7
              Hi cmbetts,

              My only interest is academic, trying to understand the variability of RNA-seq workflows as well as I can.

              Best,
              -yumpe

              Comment

              Latest Articles

              Collapse

              • 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
              • seqadmin
                The Impact of AI in Genomic Medicine
                by seqadmin



                Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
                02-26-2024, 02:07 PM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, 03-14-2024, 06:13 AM
              0 responses
              34 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-08-2024, 08:03 AM
              0 responses
              72 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-07-2024, 08:13 AM
              0 responses
              81 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-06-2024, 09:51 AM
              0 responses
              68 views
              0 likes
              Last Post seqadmin  
              Working...
              X