Computational protocol: Modulation of the Host Lipid Landscape to Promote RNA Virus Replication: The Picornavirus Encephalomyocarditis Virus Converges on the Pathway Used by Hepatitis C Virus

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Protocol publication

[…] PI4P quantification was performed for at least 40 cells for each condition, using the ImageJ software as described elsewhere []. To determine colocalization of Sec13 or calreticulin with 3AB, images were first deconvoluted using NIS advanced Research 4.3 software (Nikon) (10 iterations) and further processed using Image J as follows. Individual infected cells were outlined and a mask was created, and all signal outside the mask was cropped to exclude it from the calculations. Manders’ colocalization coefficient was calculated for at least 10 cells for each condition using the JACoP plugin [] with a manually set threshold. Colocalization of OSBP with 3A in infected cells was analyzed using ImageJ by determining Pearson’s coefficient for at least 15 cells per condition using the Coloc 2 plugin with default settings. To quantify colocalization of filipin with 3AB, images were first deconvoluted using NIS software (20 iterations), then ImageJ was used to select infected cells and the Pearson’s coefficient of colocalization for at least 15 cells per condition was calculated using the Coloc 2 plugin with default settings. […]

Pipeline specifications

Software tools ImageJ, JACoP, Coloc
Application Microscopic phenotype analysis
Organisms Encephalomyocarditis virus, Human poliovirus 1 Mahoney, Homo sapiens, Saffold virus, Viruses, Enterovirus C
Diseases Hepatitis C, Picornaviridae Infections
Chemicals Cholesterol, Phosphatidylinositols