On the optimal design of metabolic RNA labeling experiments
Fig 1
Pulse labeling experiment types to measure degradation rates.
The conventional approach as in [18] utilizes biochemical separation, which does not preserve the fraction ratio (labeled vs. unlabeled) in the read counts. Alternative novel approaches (e.g. [12]) induce reverse transcription signature events (nucleotide conversions, typically T-to-C). Individual reads can be classified by the presence or absence of this characteristic nucleotide conversions. In an ideal case, the fraction ratio is well reflected by the read counts, however in practice a relatively low 4sU incorporation rate of 1:40 has to be taken into account ([12], [9]).