Fig. 3

Linked optical phenotype and gene expression measurements verified with two species experiment. a One or 4 beads were printed to each well of a 42 by 56 nanowell array along with an alternating pattern of mouse and human cells. The number of recovered beads per nanowell position was determined by the number of unique cell barcodes mapped back to each nanowell. b When printing four beads per well, the distribution of transcripts recovered from each nanowell was calculated as a function of the number of beads recovered. The distribution of the number of transcripts originating from each bead within a nanowell was also plotted as a function of the number of beads recovered per nanowell. c Left: fluorescence data from alternating printing of Calcein Green stained human cells and Calcein Red stained mouse cells indexed by nanowell position. Right: ratio of human to mouse transcripts recovered from each nanowell based on printing four beads per nanowell. d Transcript counts by nanowell position are annotated with the green-red fluorescence ratio from the cell printed into the corresponding nanowell