Fig. 5

Deletion of IFNAR1.L1M2a.enh alters downstream transcriptional response to IFNβ. RNA sequencing of three wildtype (gray) and four IFNAR1.L1M2a.enh knockout clones (purple) during a 24 h time course of IFNβ treatment. A Likelihood Ratio Tests [48] of RNAsequencing data revealed many genes with significantly altered IFNβ responses in knockout cells compared to wildtype. Many of these genes were expected IFN stimulated genes (red) as identified by induction in wildtype cells at the 4 h timepoint [48] (Additional file 7: Table S6). Gene ontology [51] confirmed that significantly differentially responsive genes were enriched for immune-related biological processes (red). B RNA sequencing of representative expected ISGs showed a dampened initial induction in the knockout cells (purple) compared to wildtype cells (gray) and differential expression throughout the time course of IFNβ treatment according to likelihood ratio tests [48]