"strain: MG1693"	"characteristics_ch1.1"
"growth phase: Exponential"	"characteristics_ch1.2"
"Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10"	"data_processing.1"
"Adapter cutting using cutadapt, version 1.8.3, parameters -e 0.1 -O 1 -m 12"	"data_processing.2"
"Genome mapping using Bowtie, version 1.1.2, parameters for samples 1-2: -v 2 --best --strata -m 1"	"data_processing.3"
"Read counting using bedtools, version 2.17.0, parameter: -s, the middle nucleotide of each read was taken"	"data_processing.4"
"Genome_build: U00096.3"	"data_processing.5"
"Supplementary_files_format_and_content: Read counts were normalized by the length of the unique CDS per kilobase (RPKM) and the total mapped reads per million (RPM)"	"data_processing.6"
"Total RNA was extracted using TRI Reagent (Sigma Aldrich), enriched by depleting small RNAs with GeneJET Purification Kit (Fermentas) and rRNA with MICROBExpres Bacterial mRNA Enrichment Kit (Ambion) and fragmented in alkaline solution (2 mM EDTA and 100 mM Na2CO3 pH 9.2 for 40 min at 95°C) to fragments with size of 24-35 nts. For RPFS, cells were lysed by freeze-rupturing (Retch Mill) and 100 A260 units of ribosome-bound mRNA fraction were directly used for polysomal analysis or subjected to nucleolytic digestion with 10 units/µl micrococcal nuclease (Fermentas) for 10 min at room temperature in buffer with pH 9.2 (10 mM Tris pH 11 containing 50 mM NH4Cl, 10 mM MgCl2, 0.2% triton X-100, 100 µg/ml chloramphenicol and 20 mM CaCl2) to obtain the monosomal fraction. Separation was obtained by sucrose density gradient (15-50% w/v). Subsequently, 20-35-nt RNA fragments from the monosomal fraction were size selected on a denaturing 15% polyacrylamide gel."	"extract_protocol_ch1.1"
"RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009}"	"extract_protocol_ch1.2"
"Strains were grown in LB medium (Difco) supplemented with thymine (50 µg/ml) at 37ºC, unless otherwise stated. Overnight cultures of single fresh grown colonies were diluted to an initial OD600 appr. 0.03. Cultures were collected at exponential phase (OD600 appr. 0.5)."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"E. coli MG1693"	"source_name_ch1.1"
"WT exp RPF"	"title.1"
"RNA-Seq"	"library_strategy.1"
"strain: MG1693"	"characteristics_ch1.1"
"growth phase: Exponential"	"characteristics_ch1.2"
"Strains were grown in LB medium (Difco) supplemented with thymine (50 µg/ml) at 37ºC, unless otherwise stated. Overnight cultures of single fresh grown colonies were diluted to an initial OD600 appr. 0.03. Cultures were collected at exponential phase (OD600 appr. 0.5)."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"E. coli MG1693"	"source_name_ch1.1"