"The .align files have been processed using tagalign. Reads were aligned to the reference genome (Bowtie v.0.12.0) by the first 25 nt and extended to account for the linker."	"data_processing.1"
"Clarified extracts were treated with microccocal nuclease (45 enzyme units per absorbance unit of lysate at 260 nm), purified through a sucrose gradient. Ribosome-protected footprints were size selected and converted into a cDNA library for sequencing."	"extract_protocol_ch1.1"
"library strategy: Ribosome profiling"	"extract_protocol_ch1.2"
"An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Harvested by chloramphenicol pre-treatment and centrifugation; DSP treated ex vivo; Total footprints"	"source_name_ch1.1"
"DSP2_Total"	"title.1"
"The culture was incubated with 100 µg/ml of chloramphenicol for 2 min, and harvested by centrifugation. The pellet with washed and resuspended in 100 mM NH4Cl, 10 mM MgCl2, 20 mM Tris Cl, 0.4% Triton X100, 0.1% NP-40, and 100 µl/ml chloramphenicol, and flash frozen over liquid nitrogen. The frozen cell pellets were pulverized by mixer milling and thawed in 2.5 mM DSP. The crosslinking reaction was quenched with 100 mM Tris Cl 8.3."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"strain: MC4100"	"characteristics_ch1.1"
"growth stage: mid-log phase"	"characteristics_ch1.2"
"genotype/variation: MC4100 ∆tig::kan pTig-TEV-Avi"	"characteristics_ch1.3"
"An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Harvested by chloramphenicol pre-treatment and centrifugation; DSP treated ex vivo; Total footprints"	"source_name_ch1.1"
"The culture was incubated with 100 µg/ml of chloramphenicol for 2 min, and harvested by centrifugation. The pellet with washed and resuspended in 100 mM NH4Cl, 10 mM MgCl2, 20 mM Tris Cl, 0.4% Triton X100, 0.1% NP-40, and 100 µl/ml chloramphenicol, and flash frozen over liquid nitrogen. The frozen cell pellets were pulverized by mixer milling and thawed in 2.5 mM DSP. The crosslinking reaction was quenched with 100 mM Tris Cl 8.3."	"treatment_protocol_ch1.1"