Extended Data Fig. 2: Quantification of cytokine and chemokine release from RAW264.7 cells during STm infection.
After RAW264.7 cells were infected with STm for 20 hours, the conditioned media was removed and indicated cytokines and chemokines were quantified using a custom array (Biocat, GmbH). n denotes the combined data from 2 independent experiments (batches), each batch containing 2 biological replicates per condition. Box boundaries indicate the upper and lower IQR, the median is depicted by the middle boundary and whiskers represent 1.5x IQR. Relative infected/uninfected Δ (Log2) from the cytokine array are depicted within the plot for each protein. Corresponding pSILAC-AHA infected/uninfected (Log2) ratios are presented below the corresponding protein for the 20hr post-infection time-point (with the exception of TNFa, which we could only detect at 8 hpi). Non-hits and hits match perfectly between the 2 methods. Fold effect differences between pSILAC-AHA and array-based quantification are most likely due to the fact that the cytokine assay measures steady-state protein levels and pSILAC-AHA newly synthesized proteins. As expected, for more abundant proteins, measuring steady-state levels masks changes in expression dynamics. A two-sided unpaired t-test was used to calculate p..
