"Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10"	"data_processing.1"
"Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12"	"data_processing.2"
"Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-5: -v 2 --best --strata -m 1, parameters for samples 6-9: -v 3 --best --strata -m 1"	"data_processing.3"
"Read using bedtools, version 2.17.0, parameter: -s, for samples 1-5 the middle nucleotide of each read was taken, for samples 6-9 the first nucleotide was taken and the read count was assigned to the nucleotide 5' of the first nucleotide see {Kertesz, 2010} for details"	"data_processing.4"
"Read counts were normalized by million mapped reads for each nucleotide"	"data_processing.5"
"Genome_build: strain MG1655, version U00096.2, downloaded from NCBI"	"data_processing.6"
"Supplementary_files_format_and_content: Column 1 names the nucleotide in the genome, column 2 gives counts for the forward strand, column 3 for the reverse strand, columns are tab separated"	"data_processing.7"
"Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C."	"extract_protocol_ch1.1"
"RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009}"	"extract_protocol_ch1.2"
"E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media"	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"source_name_ch1.1"
"LB RPF"	"title.1"
"RNA-Seq"	"library_strategy.1"
"strain: MC4100"	"characteristics_ch1.1"
"media: LB"	"characteristics_ch1.2"
"sample type: ribosome protected"	"characteristics_ch1.3"
"E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media"	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"source_name_ch1.1"