library_construction_protocol: For bulk RNA-seq, each biological replicate came from a separate passage and was processed separately. We extracted RNA using the Zymo Direct-zol RNA Miniprep Kit (R2053). Prior to extraction and library preparation, the samples were randomized to avoid any experimental and human biases. For bulk RNA-seq, we prepared libraries using the Single Cell/Low Input RNA Library Prep Kit for Illumina. We sequenced each sample at a depth of approximately 20 million reads on a NextSeq2000 (60 base pair length) with a P3 100 kit.