SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	data_processing	Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10 PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	data_processing	Adapter cutting using cutadapt, version 1.2.1, parameters -e 0.1 -O 1 -m 12 PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	data_processing	Genome mapping using Bowtie, version 0.12.9, parameters for samples 1-5: -v 2 --best --strata -m 1, parameters for samples 6-9: -v 3 --best --strata -m 1 PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	data_processing	Read using bedtools, version 2.17.0, parameter: -s, for samples 1-5 the middle nucleotide of each read was taken, for samples 6-9 the first nucleotide was taken and the read count was assigned to the nucleotide 5[linebreak] of the first nucleotide see {Kertesz, 2010} for details PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	data_processing	Read counts were normalized by million mapped reads for each nucleotide PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	data_processing	Genome_build: strain MG1655, version U00096.2, downloaded from NCBI PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	data_processing	Supplementary_files_format_and_content: Column 1 names the nucleotide in the genome, column 2 gives counts for the forward strand, column 3 for the reverse strand, columns are tab separated PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	extract_protocol	Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	extract_protocol	RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009} PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	source_name	Escherichia coli PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	characteristics	strain: MC4100 PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	characteristics	media: LB PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	characteristics	sample type: ribosome protected PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	source_name	Escherichia coli PGCGROWTHCONDITIONS
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	PMID_26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	contact_name	Alexander,,Bartholomaeus PGCGROWTHCONDITIONS