ATAC-seq is often robust to relatively minor variations of cell number (roughly 25k to 75k for example). In general, using too few cells causes over-digestion of chromatin and appears to create a larger fraction of reads that map to inaccessible regions of the genome (i.e. noise); using too many cells causes under-digestion and creates high molecular weight fragments, which may be difficult to sequence. However, the total number of cells also sets the fundamental diversity of the sequencing library (i.e. the number of unique DNA fragments). We note that to obtain more complex libraries, larger reaction volumes or serial reactions with the same reaction volume, can be carried out.
