SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Reads were end-to-end aligned, with no mismatches allowed, to the respective draft genomes using Bowtie2 with default settings PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Reads aligning to each protein-encoding gene family with strand-specific mapping quality above 23 were counted using HTSeq-count PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Differential expression analysis was performed with R (version 3.1.1) and edgeR (version 3.8.5) (Bioconductor). PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Lowly expressed genes (<1 read per million) were removed. PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Normalization factors were calculated using a non-linear Loess model using csaw (Bioconductor) PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Tagwise dispersion was estimated using the weighted likelihood empirical Bayes method PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	A generalized linear model likelihood ratio test was performed to test for differential expression between groups (HUS vs. non-HUS) and condition (induced vs. non-induced), with FDR-adjusted p-values < 0.05 regarded as statistically significant PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: Processed data files contain raw counts for CDS genomic features, locations of genomic features are provided in associated .gtf files PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	extract_protocol	Total RNA was isolated from cell pellets using Aurum total RNA mini kit (Bio-Rad) according to the manufacturer’s instructions, and RNA quality was controlled using the RNA 6000 nano kit and 2100 Bioanalyzer (Agilent). Ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Epicentre). PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	extract_protocol	Library preparation was performed with TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina). Libraries were sequenced with 50 bp single read configuration on a HiSeq 2500 system (Illumina). PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	source_name	E. coli strain St. Olav17 PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	treatment_protocol	The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	strain: St. Olav17 PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	group (hus/non-hus): Non-HUS PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	induced/non-induced: Induced PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	genome accession: GCA_000966935 PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	Bacterial cells from an overnight culture were washed and diluted in fresh SILAC (stable isotope labeling with amino acids in cell culture) medium optimized for non-auxotrophic E. coli (Ping LY et al. J Proteome Res., 2013), before incubation at 37 °C with agitation until reaching an OD600 of approximately 0.3. PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	source_name	E. coli strain St. Olav17 PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	treatment_protocol	The exponential phase culture was split in two, and one part was induced with mitomycin C at a final concentration of 0.25 μg/ml. Both cultures were subsequently incubated at 37 °C with agitation for 1.5 hours. Bacterial cells were then spun down and resuspended in 5-10 volumes of RNA later (QIAGEN) before being frozen at -20 °C. PGCGROWTHCONDITIONS
SRR6908274	GSE112430	GSM3070058	GPL18133	PMID_30008706	50.St. Olav17.IND.nHUS	Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	contact_name	Christina,Gabrielsen,Aas PGCGROWTHCONDITIONS