"Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2"	"data_processing.1"
"Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode"	"data_processing.2"
"Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size."	"data_processing.3"
"Genome_build: NC_000913.3"	"data_processing.4"
"Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample"	"data_processing.5"
"After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp."	"extract_protocol_ch1.1"
"RNA libraries were prepared for sequencing using standard Illumina protocols"	"extract_protocol_ch1.2"
"glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2."	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"E. coli K12 MG1655"	"source_name_ch1.1"
"MG_no_te_1"	"title.1"
"RNA-Seq"	"library_strategy.1"
"strain: MG1655"	"characteristics_ch1.1"
"media: M9 minimal media w/ 0.2% glucose w/o trace elements"	"characteristics_ch1.2"
"knock-out: --"	"characteristics_ch1.3"
"glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2."	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"E. coli K12 MG1655"	"source_name_ch1.1"