barcoded_flu_pdmH1N1

Interactive plot of viral transcription and progeny production

This page provides an interactive version of figures 5A and 5B from Influenza virus transcription and progeny production are poorly correlated in single cells. Each point on this plot represents a single-influenza infected cell. You can mouse over each point to see information about the outcomes of viral infection in that cell. At the bottom of the plot, there are drop down menus to select cells with specific viral genotypes and missing viral genes.

Viral transcription and progeny production in cells infected at low MOI

Viral transcription and progeny production in cells infected at high MOI

Data available in these plots

This plot shows viral transcription on the x-axis and progeny production on the y-axis. Each point represents a single influenza-infected cell. Mousing over a point provides further information:

cell_barcode: Barcode that uniquely identifies each cell
frac_viral_UMIs: Fraction of mRNA in the cell from virus
total_UMIs: Total number of unique mRNA molecules sequenced in the cell
missing_viral_genes: List of viral genes that are not expressed in the cell
mutated_genes: List of viral genes that have any mutation
freq_supernatant: Fraction of viral barcodes in supernatant generated by the cell; represents physical progeny virions
freq_second_infection: Fraction of viral barcodes in cells infected with supernatant generated by the cell; represents infectious progeny virions
viral_mutations: List of mutations identified in the viral genes and classification of the mutation (e.g. synonymous, non-synonymous, non-coding)
mutation_support: Number of UMIs sequenced in the PacBio data supporting a consensus mutation out of all UMIs sequenced in the PacBio data for gene

How these plots were created

These plots shows the total viral transcription and progeny produced by single influenza-infected cells. Total viral transcription was calculated as the fraction of mRNA from virus in each cell. Physical progeny production was calculated as the fraction of viral barcodes in the supernatant associated with each cell among barcodes assignable to any infected cell. Infectious progeny production (right, when available) was calculated in the same way, using RNA extracted from cells infected with progeny viral supernatants.

Source data and code

The input data and code used to generate this plot are in the final_analysis.py.ipynb notebook.

This webpage was created by David Bacsik and Jesse Bloom. Thanks to Will Hannon for assistance.