SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Basecalls performed using Casava versions 1.6 or 1.7. PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Sequenced reads were trimmed for adaptor sequence. PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli genome using parameters -v 1 -m 1 --best. This allows one mismatch and reports only reads that align 1 or fewer times to the genome PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint 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. PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Genome_build: NC000913.2 PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	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
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C 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 4C. PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	Ribosome protected and total mRNA fragments were size selected via gel purification. Fragments were ligated to 5[linebreak] adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More details at MS Guo, TB Updegrove, et al, Genes Dev. (2014). PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	ribosome profiling in rich defined media PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	treatment_protocol	At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	strain: MG1655 PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	media: fully supplemented MOPS glucose media PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	molecule subtype: ribosome protected mRNA PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	Bacteria were grown at 30C with shaking (~200 rpm) in fully supplemented MOPS glucose media (Teknova) to OD420 ~0.4. Cultures were split into 4 subcultures, and grown to OD ~0.3. PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	ribosome profiling in rich defined media PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	treatment_protocol	At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS
SRR1425204	GSE58637	GSM1415872	GPL14548	PMID_25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	contact_name	Carol,A,Gross PGCGROWTHCONDITIONS