Question: My ATAC trace looks different, is it ok to proceed?
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 multinucleosome fragments. See: What are the peaks present in my ATAC library trace?
Normal variations: Some variation in the ATAC traces may be observed due to sample preservation or biological differences. The periodicity of the chromatin is still observed, although the intensity of peaks changes. It is ok to proceed with sequencing such samples.
- Single peak: Traces showing only one peak should not be sequenced. See Why does my ATAC trace only have 1 peak?
- Increased mononucleosome peak: Traces showing a mononucleosome peak that abnormally high may indicate an increase of dead/dying cells or granulocyte contamination within the sample. See How do granulocytes affect my ATAC data? Exert caution when sequencing, expect an increased number of cells to be filtered out as "non-cells". Sample prep optimization is recommended.
Products: Single Cell ATAC