Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • icanwinwyz
    Junior Member
    • Feb 2016
    • 8

    Compare bulk RNA-seq with single cell RNA-seq

    Hi everyone,
    I recently used 10X chromium techniques to do the single cell RNA-seq for my sample. I totally yielded about 3000 cells. I would like to compare the single cell transcriptome profile with the bulk RNA-seq using the same sample to check the consistency (correlation). However, 10X used the 3' sequencing strategy and produced UMI counts but bulk RNA-seq sequenced the whole transcript and produced RPKM. I would like to ask does it make sense to check their consistency with different sequencing strategy/units? If so, what is the best way to do this?

    Many thanks in advance!
  • nucacidhunter
    Jafar Jabbari
    • Jan 2013
    • 1250

    #2
    I have heard presenters stating this to convince that their single cell data is reliable. I do not see any reason for this justification because of following:

    1- Bulk RNA-seq data resulting from the same sample using polyA capture and rRNA depletion are not highly correlated

    2- Bulk RNA-seq data resulting from the same sample using two different kits are even less correlated

    3- Assuming 10pg RNA/cell your combined total RNA input would be 30 ng. Most bulk RNA-seq kits require minimum 100 ng input so the results will not be comparable.

    Comment

    • cmbetts
      Senior Member
      • Jun 2012
      • 120

      #3
      Originally posted by nucacidhunter View Post
      3- Assuming 10pg RNA/cell your combined total RNA input would be 30 ng. Most bulk RNA-seq kits require minimum 100 ng input so the results will not be comparable.
      Generally once you're >30 cells the average expression starts to converge on bulk sequencing (Prepared by the same protocol). The issue here is that you can't recreate the 10X protocol on your bulk sample. In my experience with a different 3' scRNA method, you'd be lucky to get a correlation >0.7 compared to bulk conventional RNA-Seq.

      Comment

      • nucacidhunter
        Jafar Jabbari
        • Jan 2013
        • 1250

        #4
        Originally posted by cmbetts View Post
        Generally once you're >30 cells the average expression starts to converge on bulk sequencing (Prepared by the same protocol).
        I wonder if there is any reference for this.

        Comment

        • skannan4
          Junior Member
          • Sep 2017
          • 5

          #5
          I found this paper that suggests that at >10 cells expression converges to bulk (r = 0.92). But just to follow up, do you all suggest that there is no need to run a bulk sample as QC when running single cell RNA-seq? Obviously we would like to drop the sequencing costs if possible and not needing to sequence the bulk sample would be a relief.

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Pathogen Surveillance with Advanced Genomic Tools
            by seqadmin




            The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
            03-24-2025, 11:48 AM
          • seqadmin
            New Genomics Tools and Methods Shared at AGBT 2025
            by seqadmin


            This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

            The Headliner
            The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
            03-03-2025, 01:39 PM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 03-20-2025, 05:03 AM
          0 responses
          49 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-19-2025, 07:27 AM
          0 responses
          57 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-18-2025, 12:50 PM
          0 responses
          50 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-03-2025, 01:15 PM
          0 responses
          201 views
          0 reactions
          Last Post seqadmin  
          Working...