Question: Where should I expect cells from different sample types to be located in the Peaks Targeting plot?
Answer: The Peaks Targeting plot in the web summary file shows the number of ATAC fragments for a given barcode on the x-axis and the fraction of fragments overlapping peaks on the y-axis. The fraction of fragments overlapping peaks can vary between sample types as illustrated below:
The fraction of fragments overlapping peaks can also vary based on sample storage conditions as illustrated in How does the data compare between fresh and frozen samples in the Multiome assay?.
Our publicly available Flash-Frozen Lymph Node with B Cell Lymphoma dataset is a representative example of data from a primary tissue. Although a lower fraction of fragments overlap peaks than in PBMCs, there are abundant peaks and clusters corresponding to expected cell types are still readily identified.
Barcodes with a very low fraction of fragments overlapping peaks have lost chromatin structure; the transposed fragments do not align to regions of consistently open chromatin. Reductions in chromatin structure can be caused by dead/dying cells, prolonged -80°C storage, or the presence of neutrophil-derived NETs in the sample. A few cells that have lost chromatin structure may be tolerated if the remainder have the expected targeting metrics, especially when working with primary tissues. A large percentage of cells with poor chromatin structure indicates that sample or nuclei quality requires further optimization.
Products: Single Cell Multiome ATAC+GEX, Single Cell ATAC