SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10 PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Adapter cutting using cutadapt, version 1.8.3, parameters -e 0.1 -O 1 -m 12 PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Genome mapping using Bowtie, version 1.1.2, parameters for samples 1-2: -v 2 --best --strata -m 1 PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Read counting using bedtools, version 2.17.0, parameter: -s, the middle nucleotide of each read was taken PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Genome_build: U00096.3 PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: Read counts were normalized by the length of the unique CDS per kilobase (RPKM) and the total mapped reads per million (RPM) PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	Total RNA was extracted using TRI Reagent (Sigma Aldrich), enriched by depleting small RNAs with GeneJET Purification Kit (Fermentas) and rRNA with MICROBExpres Bacterial mRNA Enrichment Kit (Ambion) and fragmented in alkaline solution (2 mM EDTA and 100 mM Na2CO3 pH 9.2 for 40 min at 95°C) to fragments with size of 24-35 nts. For RPFS, cells were lysed by freeze-rupturing (Retch Mill) and 100 A260 units of ribosome-bound mRNA fraction were directly used for polysomal analysis or subjected to nucleolytic digestion with 10 units/µl micrococcal nuclease (Fermentas) for 10 min at room temperature in buffer with pH 9.2 (10 mM Tris pH 11 containing 50 mM NH4Cl, 10 mM MgCl2, 0.2% triton X-100, 100 µg/ml chloramphenicol and 20 mM CaCl2) to obtain the monosomal fraction. Separation was obtained by sucrose density gradient (15-50% w/v). Subsequently, 20-35-nt RNA fragments from the monosomal fraction were size selected on a denaturing 15% polyacrylamide gel. PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009} PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	Strains were grown in LB medium (Difco) supplemented with thymine (50 µg/ml) at 37ºC, unless otherwise stated. Overnight cultures of single fresh grown colonies were diluted to an initial OD600 appr. 0.03. Cultures were collected at exponential phase (OD600 appr. 0.5). PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	E. coli CMA540(MG1693 ∆hfq::cat) PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	strain: CMA540(MG1693 delta_hfq::cat) PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	growth phase: Exponential PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	Strains were grown in LB medium (Difco) supplemented with thymine (50 µg/ml) at 37ºC, unless otherwise stated. Overnight cultures of single fresh grown colonies were diluted to an initial OD600 appr. 0.03. Cultures were collected at exponential phase (OD600 appr. 0.5). PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	E. coli CMA540(MG1693 ∆hfq::cat) PGCGROWTHCONDITIONS
SRR5742254	GSE100373	GSM2679700	GPL14548	PMID_29669858	Hfq mut exp RPF	The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	contact_name	Irina,,Chelysheva PGCGROWTHCONDITIONS