SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Basecalls performed using CASAVA version 1.8.2. PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Raw reads were trimmed by two nt from the 5[linebreak] end (to remove any non-templated nts added by reverse transcriptase), and were then mapped using the Burrows-Wheeler Aligner to the Escherichia coli MG1655 genome (NCBI accession NC_000913). PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Signals mapping to non-coding RNA regions were removed from the datasets (see supplementary file). PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Each dataset was normalized to reads per million per position prior to further analysis. PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	For metagene analyses (gene-segment analyses and codon-type analyses), pseudogenes and genes not represented in one or more datasets were excluded, leaving 3048 genes in the [linebreak]all genes[linebreak] dataset (see supplementary file for list of genes in [linebreak]all genes[linebreak], [linebreak]low ribosome occupancy[linebreak], and [linebreak]high ribosome occupancy[linebreak] gene sets) PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: Processed data files are WIG files with non-coding RNAs removed, normalized to reads per million per position.  Those with a [linebreak]-[linebreak] as the final character in the file name cover the minus strand of the genome; those with a [linebreak]+[linebreak] as the final character in the file name cover the plus strand of the genome. PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: Gene_lists_GEO.xls; The supplementary file contains gene lists used in data analysis. PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	RNA was extracted from samples using hot phenol. The integrity of total RNA was determined from agarose gels. PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	Library construction was performed as described in Oh et al. 2011, Cell 147(6):1295-1308 (PMCID: PMC3277850).  Briefly, fragments of total mRNA or ribosome protected mRNA fragments were size selected via gel purification, and ligated to a 5[linebreak] adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized and amplified by PCR. PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	treatment_protocol	Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	strain: EP61 PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	ethanol treatment: no ethanol exposure PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	ribosome-protected: Yes PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	treatment_protocol	Ethanol was added to 40 g/L once A600 of cultures reached 0.3.  Samples were taken prior to ethanol addition (T0), 10 min after addition (T1), and 70 min after addition (T2). Cells were harvested rapidly onto 0.2 µm filters by vacuum then flash-frozen in liquid nitrogen to arrest ribosomes.  Ribosome footprinting samples were subjected to micrococcal nuclease digestion followed by monosome isolation by sucrose gradient centrifugation. PGCGROWTHCONDITIONS
SRR1211053	GSE56372	GSM1360048	GPL14548	PMID_24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	contact_name	Rembrandt,,Haft PGCGROWTHCONDITIONS