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ATAC-seq in mouse cell lines

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  • ATAC-seq in mouse cell lines

    Hello,
    This is my first post. I have done multiple ATAC-seq libraries on human cell lines with no problems. Now I'm doing some ATAC on mouse lines.

    After 5+6 cycles, I get good nucleosome patterns on the bioanalyser and good concentration of DNA (using 100k cells) as determined by Qubit/bioanalyser.

    My major problem is - when running the qPCR side reaction after the 5 cycles of amplification, (done to determine how many more cycles to amplify) I get nothing. Zero amplification on qPCR.

    Does anyone have any suggestions?
    There are several papers which have used the same Nextera primers (the ones listed in the Buenrostro paper), on mouse cell lines.

    - I have tested two different SYBRs
    - My beads work fine (see attached imagine of bioanalyser)
    - Has always worked well on human cell lines.

    Any help greatly appreciated,
    Bw,
    Ian.
    Attached Files
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