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The amount of CUT&RUN DNA required for NG-seq analysis depends on the sensitivity of the DNA library prep kit. The typical yield for CUT&RUN DNA is 0.6 to 6 ng per reaction. Our SimpleChIP® ChIP-seq DNA Library Prep Kit for Illumina® #56795 will work with starting DNA as low as 0.5 ng. You can also increase the number of PCR cycles up to 20 to increase amplification of the library if the starting amount is too low.
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When performing CUT&RUN with downstream NG-seq analysis, one can use a normal IgG antibody enriched sample as the negative control. However, we have seen and heard from other scientists that normal IgG antibodies generate very low diversity DNA libraries and can generate what looks to be specific enrichment of genomic regions in the CUT&RUN assay, complicating your NG-seq data analysis. Instead, we recommend generating and using an input chromatin DNA sample as described in the protocol of our CUT&RUN Assay Kit #86652. This input DNA sample generates a more diverse DNA library and works better as a negative control for analysis by NG-seq.