library_construction_protocol: For bulk RNA-seq, each biological replicate came from a separate passage and was processed separately. For ATAC-seq, we lysed the cells and set up the transposition reaction with the Tn5 transposase (generously provided by our collaborators in the Kavitha Sarma lab at The Wistar Institute) at 37℃ for 30 minutes. We isolated the transposed and adaptor-ligated genomic DNA from the reaction with the Zymo DNA Clean and Concentrator­-5 Kit (Zymo #D4014) and then amplified the libraries using the custom primers described in Supplemental Table 4 (originally designed by the William Greenleaf lab at Stanford University). Prior to extraction and library preparation, the samples were randomized to avoid any experimental and human biases. For ATAC-seq, we isolated the transposed and adaptor-ligated genomic DNA from the reaction with the Zymo DNA Clean and Concentrator­-5 Kit (Zymo #D4014) and then amplified the libraries using the custom primers (originally designed by the William Greenleaf lab at Stanford University). We sequenced our libraries on a NextSeq2000 with a P3 100-cycle kit (illumina 20040559), with 60 bp paired-end reads at a depth of approximately 25 million reads per sample.