"Trimmed adaptor sequences from reads using Flexbar 2.31"	"data_processing.1"
"Mapped R1 reads in single-end mode using Bowtie2 2.1.0 with the –k 1 option"	"data_processing.2"
"The number of R1 reads mapping to each gene were counted using HTSeq 0.6.0"	"data_processing.3"
"Exact details for the full computational pipeline are available at https://github.com/wilkelab/AG3C_starvation_tc_RNAseq."	"data_processing.4"
"Genome_build: NC_012967.1 plus small RNAs as annotated in Rfam 11.0 database"	"data_processing.5"
"Supplementary_files_format_and_content: Read counts aligned to genes and noncoding Rfam features in CSV format"	"data_processing.6"
"RNAsnap"	"extract_protocol_ch1.1"
"RNA was fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Then, RNA was phosphorylated using T4 polynucleotide kinase and prepared using the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible). DNA fragments greater than 100 bp were excised from a 4% agarose gel after library preparation and recovered using the Zymoclean Gel DNA Recovery Kit (Zymo Research)."	"extract_protocol_ch1.2"
"Escherichia coli B strain REL606 was revived from a freezer stock via overnight growth in 10 ml Davis Minimal medium supplemented with limiting glucose at 0.5 g/l (DM500) in a 50 ml Erlenmeyer flask. This culture was diluted 100-fold into 50 ml fresh DM500 in a 250 ml Erlenmeyer flask and incubated for 24 hours. To initiate the experiment, these preconditioned cultures were diluted 100-fold into 50 ml fresh DM500 in multiple 250 ml Erlenmeyer flasks and grown for the specified times until harvesting cells for total RNA isolation. All growth steps were conducted with incubation at 37°C and orbital shaking at 120 r.p.m. over a one-inch diameter."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"REL606_glucose-limited minimal medium_4 hr_rRNA not depleted"	"source_name_ch1.1"
"Glucose time course, 4 hour time point, biological replicate 3, rRNA not depleted"	"title.1"
"RNA-Seq"	"library_strategy.1"
"strain: REL606"	"characteristics_ch1.1"
"time point: 4 hours"	"characteristics_ch1.2"
"molecule subtype: total RNA"	"characteristics_ch1.3"
"Escherichia coli B strain REL606 was revived from a freezer stock via overnight growth in 10 ml Davis Minimal medium supplemented with limiting glucose at 0.5 g/l (DM500) in a 50 ml Erlenmeyer flask. This culture was diluted 100-fold into 50 ml fresh DM500 in a 250 ml Erlenmeyer flask and incubated for 24 hours. To initiate the experiment, these preconditioned cultures were diluted 100-fold into 50 ml fresh DM500 in multiple 250 ml Erlenmeyer flasks and grown for the specified times until harvesting cells for total RNA isolation. All growth steps were conducted with incubation at 37°C and orbital shaking at 120 r.p.m. over a one-inch diameter."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"REL606_glucose-limited minimal medium_4 hr_rRNA not depleted"	"source_name_ch1.1"