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356141.fig.008b
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Figure 8: Density plot for CD3 (IgG1-Alexa 488), which was flagged for further evaluation by our gating quality assessment (Figure 7). The isotype gate settings look reasonable; however the MFI ratio for CD3 was very different from other markers that also had 75%–80% of their cells above the isotype gate. Looking at Figure 7, other markers with 75%–80% had MFI ratios near 5, while CD3 has an MFI ratio of 31–37. The flagging was the result of 2 cell populations for CD3, whereas most other markers stain a single population.