Landscape of transcriptional and translational changes over 22 years of bacterial adaptation

We use RNA-seq and Ribo-seq to analyze expression changes in the Long Term Evolution Experiment. By comparing expression levels between the ancestral strains and each of the evolved lines, we find that expression changes are largely parallel after 22 years of evolution, that these changes occur in specific pathways, and that known mutations may be responsible for some of the observed expression changes. 2 biological replicates each of RNA-seq and Ribo-seq of 13 E. coli cell lines. AraM and AraP refer to the 6 evolved lines of the ancestral REL606 and REL607 strains, respectively. Each file contains the data for the indicated biological replicate (rep1 or rep2), the indicated sequencing method (RNA-seq or ribo-seq), and the indicated cell lines (Ara-1-6 or Ara+1-6 and the corresponding ancestor). Code for processing the data can be found at https://github.com/shahlab/LTEE-gene-expression.