"Basecalling was performed by Torrent Suite version 5 software using the default settings."	"data_processing.1"
"Alignment to the E. coli K12 MG1655 genome sequence was performed using TMAP map4 algorithm with 5' and 3' soft-clipping and a minimum seed length of 20 nt"	"data_processing.2"
"The total sequencing base pair coverage for all annotated genes was summed for each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655."	"data_processing.3"
"Genome_build: Escherichia coli str. K-12 substr. MG1655, NCBI Reference Sequence: NC_000913.3"	"data_processing.4"
"Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in antibiotic treated to untreated cells ."	"data_processing.5"
"Briefly, hot phenol-chloroform extraction was done by mixing the cell culture in ½ volume of 99°C lysis solution (2% SDS, 16 mM EDTA, 200 mM NaCl made in RNAse-free H2O) for 10 min. The suspension was extracted twice with 1 volume of 65°C acid phenol/chloroform (pH 4.5), once in chloroform/isoamyl alcohol, and precipitated with isopropanol. Pellets were washed with 1 mL of 70% ethanol, dried and purified using QIAGEN RNeasy kit. Final RNA was eluted with 100 µL of nuclease-free water. Following purification, DNAse treatment with TURBO DNase kit was performed according to manufacturer’s manual, except that twice amount of recommended DNase inactivation reagent was used. The integrity of DNA-free RNA was analyzed on either native agarose gel or on Agilent Bioanalyzer RNA 6000 Nano chip."	"extract_protocol_ch1.1"
"Ion Xpress barcoded libraries were constructed using the Ribo-Zero Magnatic Kit (Gram-negative bacteria, Epicentre )and IonXpress RNA-seq v2 (Life Technologies) kits according to the manufacturer's directions."	"extract_protocol_ch1.2"
"E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"E. coli strain K12"	"source_name_ch1.1"
"Clindamycin_replicate_2"	"title.1"
"The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"treatment: clindamycin"	"characteristics_ch1.1"
"E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"E. coli strain K12"	"source_name_ch1.1"
"The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036."	"treatment_protocol_ch1.1"