Hello Everyone!
I am optimizing the ATAC-seq protocol currently with ProB cell lines following the Kaestner Lab protocol which is a modified version of the Buenrostro et al. protocol. I have prepared ATAC samples from 50,000 and 100,000 cells, respectively. But after library preparation, unfortunately I couldn't see any significant peak of nucleosome. Some of the samples showed a little bit of nucleosome peak but that was not very significant. Any suggestion in this regard will help!
I am also attaching the tape station profile of my samples. Please refer to page.2 to page 7 of the pdf.
Thanks in advance!