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. Author manuscript; available in PMC: 2021 Jan 27.
Published in final edited form as: Nat Methods. 2020 Jul 27;17(8):822–832. doi: 10.1038/s41592-020-0890-0

Extended Data Fig. 2. Detection efficiency after 36plex-5K O-LIT.

Extended Data Fig. 2

a) Detection efficiency without filtering after 36plex-5K O-LIT off of both streets. 95 ± 5.15% of targets are detected (n = 611 from 15 replicates). Detection efficiency from individual replicates are plotted. Error bars represent 95% bootstrap confidence interval of the mean.

b) False positive (FP) discovery rate from panel a. FP discovery rate from individual replicates are plotted. Error bars represent 95% bootstrap confidence interval of the mean.

c) Tier 1 detection efficiency after 36plex-5K O-LIT off of Mainstreet (orange, 61.93 ± 12%, n = 53 from 2 replicates) versus off of both streets (blue, 62.17% ± 6.68%, n = 611 cells from 15 replicates). Detection efficiency from individual replicates are plotted. Error bars represent 95% bootstrap confidence interval of the mean.

d) FP discovery rate from panel c. Using Mainstreet = 8.64% and using both streets = 5.29%. FP discovery rate from individual replicates are plotted. Error bars represent 95% bootstrap confidence interval of the mean.

e) Tier 2 detection efficiency after 36plex-5K off of Mainstreet (orange, 92.3% ± 3.42% from 53 cells from 2 replicates) versus off of both streets (blue, 80.19 ± 7.29%, n = 611 cells from 15 replicates). Detection efficiency from individual replicates are plotted. Error bars represent 95% bootstrap confidence interval of the mean.

f) Detection efficiency after 36plex-5K O-LIT off of both streets for individual cells from 15 replicates in panel e.

g) Percentage of cells displaying a range of efficiencies of barcode detection after 36plex-5K O-LIT off of both streets. Data taken from panel e.

h) Principal component analysis showing lack of batch effect in 36plex datasets (n = 1171 cells from 15 36plex-5K O-LIT replicates and 8 36plex-1K O-eLIT replicates).