SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	RNA-seq data were mapped to the E. coli O157:H7 Sakai genome using the Subjunc aligner program from the Subread package (v1.4.6)   (http://bioinf.wehi.edu.au/subread/). PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	The alignment Bam files were compared against the gene annotation general feature format (GFF) file, and raw counts for each gene were  generated using the featureCounts tool from Subread. The raw counts data of the expressed genes was normalized for RNA composition using the trimmed mean of M values (TMM) method (http://www.ncbi.nlm.nih.gov/pubmed/20196867) from the Empirical analysis of Digital Gene Expression Data in R (EdgeR) package   (https://bioconductor.org/packages/release/bioc/html/edgeR.html), then transformed to log2CPM (counts per million) values using the voom method   (http://www.ncbi.nlm.nih.gov/pubmed/24485249) from the R LIMMA package  (https://bioconductor.org/packages/release/bioc/html/limma.html). PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Next, a linear model was built for each comparison using the R LIMMA package and statistics for differential expression analysis were computed. To filter for differential expression, two fold or three-fold change with a FDR ≤0.05 were used as the threshold. PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Functional annotation was done using the Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resources 6.7, NIAID, NIH (http://david.abcc.ncifcrf.gov). PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	extract_protocol	Total RNA samples were isolated using RNAzol RT (Molecular Research Center) by following manufature[linebreak]s instructions. Contaminating DNA was   removed from RNA samples by DNase I digestion using the TURBO DNA-free kit (Ambion). PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	extract_protocol	RNA libraries were prepared for sequencing using standard Illumina protocols; rRNAs were removed by Ribozero (gram negative), libraries were prepared using TruSeq protocol. PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	PA20 cultures for RNA-seq were grown on T-agar with and without added Sulfamethoxazole-  Trimethoprim at designated levels for the indicated times and temperatures. Working stocks were tested and maintained using LB (Miller formulation) or LB agar. Plasmid pSE380 derivatives were induced by IPTG. PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	source_name	PA20 cultures PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	incubation time: 5 hr PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	ug/ml smx / ug/ml tm: 540/108 (27x) PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	PA20 cultures for RNA-seq were grown on T-agar with and without added Sulfamethoxazole-  Trimethoprim at designated levels for the indicated times and temperatures. Working stocks were tested and maintained using LB (Miller formulation) or LB agar. Plasmid pSE380 derivatives were induced by IPTG. PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	source_name	PA20 cultures PGCGROWTHCONDITIONS
SRR2299395SRR5016659	GSE110255	GSM2983261	GPL18133	PMID_29718957	T5_27x_1	Sulfamethoxazole – Trimethoprim represses csgD but 2 maintains virulence genes at 30°C in a clinical 3 Escherichia coli O157:H7 isolate	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	contact_name	Gaylen,C,Ulrich PGCGROWTHCONDITIONS