Contamination of 4sU labeled RNA with unlabeled RNA. (A) Yield of labeled RNA at 4sU pulses of different length in 3T9 mouse fibroblast cells. (B) A magnification of A. (C) Log likelihood score for the fit of four alternative models, considering constant (k) or exponential (exp) 4sU incorporation rates, combined with a contamination that is absent (−), constant (k), or linear to the 4sU pulse length (k + a × t). P-values of the indicated log likelihood-ratio tests are reported. (D) The estimated trend of 4sU incorporation based on the green model in panel A. (E) Changes in ROC areas under the curve (AUC) and in Spearman's correlation following the introduction of 30% contamination in simulated data.
