SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	data_processing	For the whole-transcriptome analysis, sequencing was verified using FASTQC (version 0.11.2) to confirm base-call quality in each indexed file. PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	data_processing	Indices corresponding to the same sample were merged, and then uploaded to a cloud-based variant of Galaxy named RNA23 Rocket PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	data_processing	Using Bowtie2 (version 2.0.2), sequenced reads were mapped to an EPEC O127:H6 reference genome (EMBL/GenBank accession codes FM180568, FM180569, and FM180570). PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	data_processing	Mapped reads were quality checked with SAMstat (version 1.08), and transcripts were assembled in Cufflinks (version 2.0.2) PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	data_processing	Differential gene expression (DGE) was then performed on fragments per kilobase mapped (FPKM) values in Cufflinks’ Cuffdiff package (version 0.0.7). PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	data_processing	DGE analysis used a false-discovery rate (FDR) of 0.10. PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	data_processing	Subsequent data visualizations were performed in R (version 3.1.2) using the cummeRbund package (version 3.0) PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	data_processing	Genome_build: FM180568 PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	data_processing	Genome_build: FM180569 PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	data_processing	Genome_build: FM180570 PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	data_processing	Supplementary_files_format_and_content: bedgraph: Data presented in a 4 column BED format, of which the first column is the chromosome, the second column is the start position of the chromosome, the third column is the end position, and the fourth column is the fragments per kilobase mapped (FPKM) for that sample. Chromosome positions are specified as 0-relative. The first chromosome position is 0. The last position in a chromosome of length N would be N - 1. Only positions specified have data. Positions not specified do not have data and will not be graphed. All positions specified in the input data are in numerical order. PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	data_processing	Supplementary_files_format_and_content: tabular: Tabular data that informs the excel spreadsheet. The data are averaged across the three samples per strain. Both averaged strain data are presented for each gene on the same line. Data contain gene ID, gene number, locus, fragments per kilobase mapped (FPKM) for WT and mutant strains, log2(fold-change) relative epxression of WT over mutant strains, test-statistic, p-value, q-value, and significance analyzed via the cummeRbund package in R whereby a q-value of <0.05 is considered significant. PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	data_processing	Supplementary_files_format_and_content: xls: The data are averaged across the three samples per strain. Both averaged strain data are presented for each gene on the same line. Excel spreadsheet containing gene ID, gene number, locus, fragments per kilobase mapped (FPKM) for WT and mutant strains, log2(fold-change) relative epxression of WT over mutant strains, test-statistic, p-value, q-value, and significance analyzed via the cummeRbund package in R whereby a q-value of <0.05 is considered significant. PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	extract_protocol	Samples were diluted 1:1 in RNA Protect (Qiagen, Carlsbad, CA) to inhibit RNase activity and then centrifuged (5000 x g, 10 min). Pellets were resuspended in TE/lysozyme (10 mg/ml lysozyme, 0.5% SDS, pH 8.0) with added proteinase K (1.5 mg/ml). RNA was isolated using Qiagen’s RNeasy kit according to manufacturer instructions with slight modification. Before centrifugation, β-mercaptoethanol was added to RNeasy kit buffer RLT (10% v/v). Additionally, during the wash step RNase-free DNase (Qiagen, Carlsbad, CA) was diluted in RNeasy kit buffer RDD (310 Kunitz units/mL), added to the purification column, and incubated for 15 minutes at room temperature (RT). After isolation, spectrophotometric NanoDrop (NanoDrop 1000 v3.8.1; Thermo Fisher) curves were obtained for each total RNA sample and verified for purity, as defined by absorbance ratios at 260/280 nm and 260/230 nm. Total RNA samples were sent to Oregon State University’s Center for Genome Research and Biocomputing. RNA integrity (RIN) measurements were taken using an Agilent Bioanalyzer, resulting in RIN scores of 10, out of a possible 10, for each sample. Ribosomal RNA was depleted using the RiboZero rRNA removal kit (Life Technologies, Eugene, OR). PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	extract_protocol	Resulting mRNA was reverse-transcribed to cDNA libraries via SuperScript III First Strand reverse transcription kit (Invitrogen, Carlsbad, CA, 18080051) as per the manufacturer’s instructions. The cDNA libraries were multiplexed to distinguish replicates from one another, barcoded for sequencing, and then amplified with random hexamers for 15 PCR cycles. Transcripts were sequenced for 50 bases in single-end fashion within one lane of an Illumina Hiseq 2000 flow cell. This yielded roughly 30 million reads per sample. PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	growth_protocol	LB (5 ml) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at 37°C with 225 rpm shaking. Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at 37°C with 225 rpm shaking to mid-exponential phase (OD600 0.3-0.5). PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	source_name	Whole bacterial cell RNA transcriptome PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	treatment_protocol	Incubation and RNA harvesting were carried out for all samples simultaneously and under RNase-free conditions to minimize biological variability in gene expression between each sample. Bacterial concentrations were equalized to the same density (by OD600). PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	characteristics	strain: JPEP22 PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	characteristics	genotype/variation: {delta}perC::kanR, coisogenic to WT PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	characteristics	source: Bustamante et al., 2011 PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	growth_protocol	LB (5 ml) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at 37°C with 225 rpm shaking. Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at 37°C with 225 rpm shaking to mid-exponential phase (OD600 0.3-0.5). PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	source_name	Whole bacterial cell RNA transcriptome PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	treatment_protocol	Incubation and RNA harvesting were carried out for all samples simultaneously and under RNase-free conditions to minimize biological variability in gene expression between each sample. Bacterial concentrations were equalized to the same density (by OD600). PGCGROWTHCONDITIONS
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	PMID_28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	contact_name	Jay,,Mellies PGCGROWTHCONDITIONS