SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Remaining linker-1 reads (CTGTAGGCACCATCAAT) were removed from fastq files using fastx_clipper PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Reads were aligned to E.coli rRNA and tRNA using Bowtie v.0.12.0 allowing for one mismatch and reads aligning to more than one position in the genome were randomly assigned to one of those positions PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	The remaining reads were aligned to genome using Bowtie v.0.12.0 allowing for one mismatch and reads aligning in more than one position in the genome were discarded PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	The aligned reads were converted to BAM files and sorted and indexed using SAMtools PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Wiggle files were created by center mapping the reads between 20-40bps. Using a 10bp trim on either side of the read then mapping the read across the remaining location using Plastid. PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Genome_build: NC_000913 PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: Bedgraph wiggle files were created for each sample and replicate for all reads aligned to the genome after computational rRNA and tRNA subtraction PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	Whole cell lysates were clarified by brief centrifugation. Ribosome footprints were created using Mnase digestion (45 enzyme units per absorbance unit of lysate at 260nm). Using sucrose gradients the monosome fraction of lysate was isolated and footprints were size selected and converted to a cDNA library. Total RNA was extracted from purified lysate for a simultaneous RNA-seq library production for total RNA samples. Small RNA and ribosomal RNA subtraction was performed in total RNA samples using MEGAClear (ThermoFisher) and MicrobExpress (ThermoFisher) kits. Subtracted total RNA was then subjected to alkaline fragmentation prior to library preparation. PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	A Linker-1 adapter (IDT) was ligated onto the 3[linebreak] end of size selected RNA fragments, either ribosome footprints or fragmented total RNA. A cDNA library was created using Superscript III (ThermoFisher). After gel purification of the cDNA library all ssDNA fragments were circularized using CircLigase (Epicentre). For ribosome profiling samples rRNA containing circles were depleted using oligo-biotin  and streptavidin coupled Dynabeads (ThermoFisher) subtraction. A PCR amplification off the circles using HF Phusion (NEB) completed the libraries by adding Illumina Tru-Seq adapters and a unique index for each sample. PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	whole cell lysate PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	treatment_protocol	Cells from each strain were rapidly harvested by filtration and lysate was produced by pulverization of liquid nitrogen cooled samples. PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	strain: K12 MG1655 prfB-Bstrain allele PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	whole cell lysate PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	treatment_protocol	Cells from each strain were rapidly harvested by filtration and lysate was produced by pulverization of liquid nitrogen cooled samples. PGCGROWTHCONDITIONS
SRR4421271	GSE88725	GSM2344789	GPL14548	PMID_28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	contact_name	Natalie,,Baggett PGCGROWTHCONDITIONS