has2k1/plotnine: v0.7.0

Kibirige, Hassan; Lamp, Greg; Katins, Jan; gdowding,; Austin, O; matthias-k,; Funnell, Tyler; Finkernagel, Florian; Arnfred, Jonas; Blanchard, Dan; Astanin, Sergey; Chiang, Eric P.; Kishimoto, Paul Natsuo; Sheehan, Evan; stonebig,; Willers, Bernard; Gibboni, Robert; smutch,; Halchenko, Yaroslav; Pavel,; King, Brian; Rk, Min; Collins, John J.; zachcp,; ANTHONY, Anthony; Koopman, Bevan; Becker, D.; Brown, Dan; Brian, Duncan; guoci,

doi:10.5281/zenodo.3878645

Cited by 2 publications

(1 citation statement)

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“…The data were visualized in Jupyter notebook RRID: SCR_018416 Version 4.6.3 ( https://github.com/jbloomlab/barcoded_flu_pdmH1N1/blob/main/final_analysis.py.ipynb ). We used custom Python code utilizing a combination of plotnine ( https://github.com/has2k1/plotnine ; Kibirige, 2023 ; Kibirige et al, 2020 ) and altair ( https://github.com/altair-viz/altair ; Altair, 2023 ). An R script utilizing gggenes ( https://github.com/wilkox/gggenes ; Wilkins, 2020 ) was used to plot the complete viral genomes of infected cells.…”

Section: Methodsmentioning

confidence: 99%

Influenza virus transcription and progeny production are poorly correlated in single cells

Bacsik

Dadonaite

Butler

et al. 2023

eLife

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The ultimate success of a viral infection at the cellular level is determined by the number of progeny virions produced. However, most single-cell studies of infection quantify the expression of viral transcripts and proteins, rather than the amount of progeny virions released from infected cells. Here we overcome this limitation by simultaneously measuring transcription and progeny production from single influenza-virus-infected cells by embedding nucleotide barcodes in the viral genome. We find that viral transcription and progeny production are poorly correlated in single cells. The cells that transcribe the most viral mRNA do not produce the most viral progeny, and often represent aberrant infections that fail to express the influenza NS gene. However, only some of the discrepancy between transcription and progeny production can be explained by viral gene absence or mutations: there is also a wide range of progeny production among cells infected by complete unmutated virions. Overall, our results show that viral transcription is a relatively poor predictor of an infected cell’s contribution to the progeny population.

show abstract

Section: Methodsmentioning

confidence: 99%

Influenza virus transcription and progeny production are poorly correlated in single cells

Bacsik

Dadonaite

Butler

et al. 2023

eLife

View full text Add to dashboard Cite

show abstract

Influenza virus transcription and progeny production are poorly correlated in single cells

Bacsik,

Dadonaite,

Butler

et al. 2023

eLife

View full text Add to dashboard Cite

The ultimate success of a viral infection at the cellular level is determined by the number of progeny virions produced. However, most single-cell studies of infection quantify the expression of viral transcripts and proteins, rather than the amount of progeny virions released from infected cells. Here, we overcome this limitation by simultaneously measuring transcription and progeny production from single influenza virus-infected cells by embedding nucleotide barcodes in the viral genome. We find that viral transcription and progeny production are poorly correlated in single cells. The cells that transcribe the most viral mRNA do not produce the most viral progeny and often represent aberrant infections that fail to express the influenza NS gene. However, only some of the discrepancy between transcription and progeny production can be explained by viral gene absence or mutations: there is also a wide range of progeny production among cells infected by complete unmutated virions. Overall, our results show that viral transcription is a relatively poor predictor of an infected cell’s contribution to the progeny population.

show abstract

has2k1/plotnine: v0.7.0

Cited by 2 publications

References 0 publications

Influenza virus transcription and progeny production are poorly correlated in single cells

Influenza virus transcription and progeny production are poorly correlated in single cells

Influenza virus transcription and progeny production are poorly correlated in single cells

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