SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Vertis Biotechnologie AG bioinformatics department did a preliminary analysis of the high-throughput sequencing results which included the mapping of the reads against E. coli genome (NC_000913 downloaded from NCBI genome database). PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	We then used the mapped files to run Cufflinks (estimates the relative abundance of the transcripts) and after Cuffdiff to find significant changes in transcript expression when comparing two samples (Trapnell, Williams et al. 2010). PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Genome_build: ASM584v2 PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample … PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	RNA was isolated following cell lysis and phenol:chloroform extraction as previously described (Andrade, Pobre et al. 2012). After precipitation step in ethanol and 300 mM sodium acetate, RNA was resuspended in MilliQ-water. The integrity of RNA samples was evaluated by agarose gel electrophoresis. Turbo DNase (Ambion) treatment was used to remove contaminant DNA. PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	RNA libraries were prepared for sequencing by the company Vertis Biotechnologie AG in Germany PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	Overnight cultures from isolated colonies were diluted in fresh medium to an initial OD600~0.03 and grown to exponential phase (OD600~0.3) at 37ºC, with shaking at 200 rpm in Luria-Bertani (LB) medium supplemented with thymine (50 mg ml-1). When required, antibiotics were present at the following concentrations: kanamycin, 50 mg ml-1; tetracycline, 20 mg ml-1; streptomycin/spectinomycin 20 µg ml-1. PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Culture cells PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	strain: K12-MG1693 PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	growth phase: Exponential Phase PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	genotype: RNase R mutant PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	Overnight cultures from isolated colonies were diluted in fresh medium to an initial OD600~0.03 and grown to exponential phase (OD600~0.3) at 37ºC, with shaking at 200 rpm in Luria-Bertani (LB) medium supplemented with thymine (50 mg ml-1). When required, antibiotics were present at the following concentrations: kanamycin, 50 mg ml-1; tetracycline, 20 mg ml-1; streptomycin/spectinomycin 20 µg ml-1. PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Culture cells PGCGROWTHCONDITIONS
SRR1536588	GSE60107	GSM1465037	GPL14548	PMID_25757888PMID_30486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	contact_name	Cecilia,M.,Arraiano PGCGROWTHCONDITIONS