Figure 4.

Read count pooled from the four padlock probes in the 16-plex and 256-plex assay conditions (a) Actb reads count per cell in the 16-plex assay conditions (i.e. after two hybridization cycles) for on-chip and off-chip protocol. Sequencing accuracy defined as the ratio of the expected to the sum of expected and unexpected reads, essentially the contribution of the blue bar to the total height of the stack bar, is 90% and 95% for on-chip and off-chip respectively. (b) Reads from (a) displayed over DAPI staining of cells’ nuclei. (c) Actb reads count per cell in the 256-plex assay conditions (i.e. after four hybridization cycles). Sequencing accuracy is 64% and 87% for on-chip and off-chip respectively. (d) Reads from (c) displayed over DAPI staining of cells’ nuclei. In (a,b) the reads from the four different padlock probes, all targeting the same epitope of Actb, are pooled together. Scale bars are 5 µm.