"strain: K-12"	"characteristics_ch1.1"
"genotype/variation: K100R"	"characteristics_ch1.2"
"media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose"	"characteristics_ch1.3"
"growth phase: Late exponential/Early stationary (OD ~1.8)"	"characteristics_ch1.4"
"Base calls were made using MiSeq Reporter v. 2.6.2.1"	"data_processing.1"
"Low quality reads were trimmed with CutAdapt"	"data_processing.2"
"Adpater sequences were clipped with CutAdapt"	"data_processing.3"
"The resulting reads were mapped to the reference genome of Escherichia coli str. K-12 substr. MG1655 using Tophat2 using the following parameters, --GTF --library type fr-secondstrand"	"data_processing.4"
"Mapped reads were counted using the Python package HTSeq (v. 0.6.1) using the following parameters; htseq-count -m union -r pos -i gene_name -a 10"	"data_processing.5"
"Differential expression testing between sample groups was performed in Rstudio (v. 1.0.36) using DESeq2 (v.1.14.1)"	"data_processing.6"
"Genome_build: Escherichia coli str. K-12 substr. MG1655"	"data_processing.7"
"Supplementary_files_format_and_content: text files containing gene counts output by htseq-count"	"data_processing.8"
"Supplementary_files_format_and_content: Comma separated value files include log-fold changes and associated p-values for each comparison made"	"data_processing.9"
"Cell pellets were lysed in Tissue and Cell lysis solution (EpiCentre) and proteinase K. RNA was isolated and DNase treated using the RNeasy Kit (Qiagen) using the manufacturer’s protocol. The amount of total RNA in each sample was quantified using the Qubit 2.0 Flurometer (Life Technologies) and quality was assessed using the RNA6000 Nano Chip on the Bioanalyzer 2100 (Agilent)."	"extract_protocol_ch1.1"
"rRNA depletion, fragmentation, reverse transcription, tagging, barcoding, limited cycle PCR (Illumina)"	"extract_protocol_ch1.2"
"ScriptSeq v2 Complete Kit (EpiCentre)"	"extract_protocol_ch1.3"
"Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"K100R"	"source_name_ch1.1"
"K100R rep 2"	"title.1"
"RNA-Seq"	"library_strategy.1"
"strain: K-12"	"characteristics_ch1.1"
"genotype/variation: K100R"	"characteristics_ch1.2"
"media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose"	"characteristics_ch1.3"
"growth phase: Late exponential/Early stationary (OD ~1.8)"	"characteristics_ch1.4"
"Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"K100R"	"source_name_ch1.1"