Stochastic Analysis of the RT-PCR Process in Single-Cell RNA-Seq
Por:
Vazquez-Jimenez, Aaron, Resendis-Antonio, Osbaldo
Publicada:
1 oct 2021
Resumen:
The single-cell RNA-seq allows exploring the transcriptome for one cell
at a time. By doing so, cellular regulation is pictured. One limitation
is the dropout events phenomenon, where a gene is observed at a low or
moderate expression level in one cell but not detected in another.
Dropouts obscure legitimate biological heterogeneity leading to the
description of a small fraction of the meaningful relations. We used a
stochastic approach to model the Reverse Transcription Polymerase Chain
Reaction (RT-PCR) kinetic, in which we contemplated the temperature
profile, RT-PCR duration, and reaction rates. By studying the underlying
biochemical processes of RT-PCR, using a computational and analytical
framework, we show a minimal amount of RNA to avoid dropout events. We
further use this fact to characterize the limits in the dispersion
reduction. Dispersion asymptotically decreases as the RNA initial value
increases. Despite always being a basal dispersion, their decreasing
speed is modulated mainly by the degradation rates, particularly for the
RNA. We concluded that the critical step into the RT-PCR is the RT phase
due to the fragile nature of the RNA. We propose that limiting RNA
degradation might ensure that the portraited transcriptional landscape
is unbiased by technical error.
Filiaciones:
Vazquez-Jimenez, Aaron:
Inst Nacl Med Genom, Human Syst Biol Lab, Periferico Sur 4809, Mexico City 14610, DF, Mexico
Resendis-Antonio, Osbaldo:
Inst Nacl Med Genom, Human Syst Biol Lab, Periferico Sur 4809, Mexico City 14610, DF, Mexico
Univ Nacl Autonoma Mexico, Coordinac Invest Cient Red Apoyo Invest, Vasco de Quiroga 15, Mexico City 14080, DF, Mexico
gold, Gold
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