Computational protocol: Adopting the rapamycin trapping assay to track the trafficking of murine MHC class I alleles, H-2Kb

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Protocol publication

[…] For quantification, the plugin JACoP version 2.0 was used in imageJ []. The pearson’s coefficient of the intensities of the two channels was plotted by the red channel on the x-coordinate (organelle markers) and the green channel on the y-coordinate (H2-Kb). Pearson’s coefficient provides an approximate of the rate of linear association between the two used fluorochromes. Its values range between −1 and 1 with zero no correlation and negative values for negative correlation. Region of interest (ROI) from selected cells was cropped, then channels were split, and quantified using JACoP plugin. […]

Pipeline specifications

Software tools JACoP, ImageJ
Application Microscopic phenotype analysis
Organisms Mus musculus, Homo sapiens
Chemicals Sirolimus