Below are data from a head-to-head comparison of Active Motif’s MethylCollector™ Ultra kit vs. Invitrogen’s MethylMiner™ Methylated DNA Enrichment Kit. To learn more about MethylMiner™ kits, view out Frequently Asked Questions.

  • The MethylMiner™ kit captures 99% of hypermethylated PLAU promoter from MCF-7 DNA.
  • The MethylCollector™ Ultra kit captures less than half (46%) of the same locus and loses a majority in the unbound (19%) and wash (35%) fractions.
  • The MethylMiner™ kit captures a small portion (10%) of the lightly methylated PLAU promoter from MDA-MB-231 cells.
  • The MethylCollector™ Ultra kit shows no capture from MDA-MB-231 DNA.
  • MethylMiner™ kit wash fractions have minimal DNA in contrast to MethylCollector™ Ultra kit wash fractions.

Figure 1. Capture of methylated DNA from two breast cancer cell lines.
Following each manufacturer’s protocol, 500 ng of mechanically fragmented DNA (100–600 bp) was captured and eluted. Elution was with proteinase K for the MethylCollector™ Ultra kit and with high-salt (2 M NaCl) buffer for the MethylMiner™ kit.  For reference, the methylation at each CpG, as measured by bisulfite cloning and sequencing, is shown in Part B.


  • Neither kit captures much of the nonmethylated ESR1 exon 1 from MCF-7 DNA.
  • The MethylMiner™ kit captures much of the lightly methylated ESR1 exon 1 DNA (55%) from MDA-MB-231.
  • The MethylCollector™ Ultra kit poorly captures the lightly methylated ESR1 exon 1 DNA (2%) from MDA-MB-231.

Figure 2. Capture of methylated DNA from two breast cancer cell lines.
Following each manufacturer’s protocol, 500 ng of mechanically fragmented DNA (100–600 bp) was captured and eluted. Elution was with proteinase K for the MethylCollector™ Ultra kit and with high-salt (2 M NaCl) buffer for the MethylMiner™ Kit.  For reference, the methylation at each CpG, as measured by biulfite cloning and sequencing, is showin in Part B.


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