"infection: T7"	"characteristics_ch1.1"
"t7 strain: evolved"	"characteristics_ch1.2"
"t7 genotype: evolved, codon-deoptimized gene 10"	"characteristics_ch1.3"
"time: 9 min post-infection"	"characteristics_ch1.4"
"pseudoalignment and quantitation with kallisto v0.42.5 with parameters --single -l 450 -s 250"	"data_processing.1"
"Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded and evolved strains"	"data_processing.2"
"Supplementary_files_format_and_content: tab-delimitted text files contain TPM (transcripts per million) values for each sample"	"data_processing.3"
"RNA was isolated using Trizol reagent (Thermo Fisher Scientific)"	"extract_protocol_ch1.1"
"Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent)."	"extract_protocol_ch1.2"
"Escherichia coli"	"organism_ch1.1"
"cell culture"	"source_name_ch1.1"
"evolved 9min rep7"	"title.1"
"RNA-Seq"	"library_strategy.1"
"infection: T7"	"characteristics_ch1.1"
"t7 strain: evolved"	"characteristics_ch1.2"
"t7 genotype: evolved, codon-deoptimized gene 10"	"characteristics_ch1.3"
"time: 9 min post-infection"	"characteristics_ch1.4"
"Escherichia coli"	"organism_ch1.1"
"cell culture"	"source_name_ch1.1"