Differential gene expression analysis

Differential gene expression analysis in TRAP samples (including calculation of gene enrichment and depletion, relative to tissue homogenate RNA) was performed using DESeq2 (v1.36.0, RRID:SCR_015687) in R (v4.2.1, RRID:SCR_001905) with Bioconductor (v3.15, RRID:SCR_006442). Adaptive shrinkage of log fold change estimates was performed using ashr. The following settings were changed from defaults: minReplicatesForReplace = Inf, cooksCutoff = Inf, filterFun = ihw, lfcThreshold = log₂(1.05). Genes were classed as significantly differentially expressed with an FDR-adjust P value < 0.01. Protein-protein interactions were obtained using STRINGdb (version 11) with a minimum confidence threshold of 0.4.