SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	data_processing	Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	data_processing	Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	data_processing	Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded. PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	data_processing	The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1. PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	data_processing	Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5[linebreak] of the 5[linebreak] end of the read. PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	data_processing	Genome_build: NC000913.2 PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	data_processing	Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details). PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction. PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	mRNA fragments were size selected via gel purification, and ligated to 5[linebreak] adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014). PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	source_name	MG1655 PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	treatment_protocol	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	characteristics	strain background: MG1655 PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype/variation: wild type PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	characteristics	temperature: 10°C PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	characteristics	molecule subtype: Ribosome protected mRNA PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	source_name	MG1655 PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	treatment_protocol	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	PMID_29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	contact_name	Yan,,Zhang PGCGROWTHCONDITIONS