To identify Drop-seq beads that hybridized mRNA from intact cells versus mRNAs in solution, we plotted total library size (UMI counts) versus the library fraction corresponding to mitochondrial and ribosomal transcripts. We reasoned that since mitochondrial/ribosomal transcripts are present at high-concentration in the suspension, their abundance could serve as a signature for non-cellular (ie background/ambient) hybridization. To identify beads containing cellular libraries, we plotted the library size versus library fraction attributed to mitochondrial/ribosomal transcripts.
