"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 cushion, and affinity purified via TF. Ribosome-protected footprints were size selected and converted into a cDNA library for sequencing."	"extract_protocol_ch1.1"
"library strategy: Selective 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 rapid filtration; EDC treated ex vivo; Affinity purified TF crosslinked RNC footprints"	"source_name_ch1.1"
"EDC1_AP"	"title.1"
"Cells were flash frozen in liquid nitrogen after the media was rapidly filtered. Frozen cells were pulverized by mixer milling and thawed in 20 mM EDC, pH 5.8. The crosslinking reaction was quenched with 250 mM glycine, 100 mM Tris Cl 8.0, and 4 mM NaHCO3."	"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 rapid filtration; EDC treated ex vivo; Affinity purified TF crosslinked RNC footprints"	"source_name_ch1.1"
"Cells were flash frozen in liquid nitrogen after the media was rapidly filtered. Frozen cells were pulverized by mixer milling and thawed in 20 mM EDC, pH 5.8. The crosslinking reaction was quenched with 250 mM glycine, 100 mM Tris Cl 8.0, and 4 mM NaHCO3."	"treatment_protocol_ch1.1"