I performed ATAC-seq with Hela cell but it didn't work.
qPCR graphs were good to calculate the number of additional PCR cycles but, when i assessed the quality of purified libraries with tapestation, the libraries's concentration were too low to detect ( but when i measure the libraries with nanodrop, all sample had over 10 ng/ul conc.)
I attached my protocol (from Kaestner lab) and my tapestation results.
ㅠㅠ Why this protocol did't work?
I would first advise you to measure concentration of your ATAC-seq libraries using Qubit and not nanodrop. Nanodrop tends to overestimate concentrations since it's not specific for double stranded DNA like Qubit. Second, based on the band position from tapestation it seems like you have a single ~200bp product. What you would expect are multiple products of different sizes that correspond to nucleosome-free DNA (~200bp) and 1-2-3-multi- nucleosomal DNA. Based on this my guess is that your ratio between Tn5 transposase and nuclei is not optimal, or your tagmentation time was too long. You should always optimize ratio between the number of input cells and transposase and test different tagmentation times, especially if you are using new type of cells. Finally, for the future it would be more informative to see tapestation traces.
Good luck!
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