SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping. PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	For each uniquely mapped fragment (ribozero treated samples) or all mapped fragments (total RNA samples), at all aligned positions a count was added. PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Counts were depth normalized to a pseudo-reference sample calculated from all samples (ribozero treated samples) or using counts per million counts (total RNA samples). PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	For ribozero treated samples, counts at all positions were log2 transformed and a cleavage ratio was calculated (+ MazF - empty vector) for assessing MazF cleavage in transcripts. PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Genome_build: NCBI reference sequence: NC_000913.2 PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: 5m_ribozero_counts_cleavage_ratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each ribozero treated sample as well as the average cleavage ratio calculated from all samples. total_RNA_rpm.csv.gz is a list of sequencing depth-normalized counts for every genomic position at both strans for all total RNA samples. PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	extract_protocol	RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo). PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	extract_protocol	See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols. PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	source_name	Bacterial liquid culture PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	strain: MG1655 delta_mazF PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	plasmid: pBAD30-MazF PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	ribozero: Yes PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	ercc spike-in: No PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	time induction: 5 minutes PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	source_name	Bacterial liquid culture PGCGROWTHCONDITIONS
SRR6322035	GSE107327	GSM2864855	GPL21222	PMID_29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	contact_name	Peter,,Culviner PGCGROWTHCONDITIONS