Question: What are the peaks present in my ATAC library trace?
Answer: A representative trace for an ATAC library can be found in the Chromium Single Cell ATAC Reagent Kits User Guide.
The peaks of the final trace are indicative of the periodicity of the chromatin structure and show nucleosome-free, mononucleosome, dinucleosome and multinucleated fragments. The peaks occur at a frequency of 150-180bp, concordant with the length of DNA wrapped around each nucleosome. The intensity of these peaks may vary due to sample type, nuclei load, its level of open chromatin and the platform being used for QC. Below are representative traces an ATAC library prepared from PBMCs from a healthy human donor run on the Bioanalyzer and the TapeStation.
Note, that an adapter dimer peak at 150bp may also be present. However, this dimer does not sequence well and makes up <0.1% of the total reads.
Products: Single Cell ATAC