SRR427120	GSE36248	GSM885047	GPL10328	PMID_	no treatment	Transcriptome mapping of blaCMY-2 positive IncA/C plasmid pAR060302	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	data_processing	cDNA reads were trimmed so that the quality at each base position was above 30 (~15-20 bp) and then mapped either to the E. coli K-12 MG1655 published genome sequence (Genbank accession no. NC_000913) or to the pAR060302 published sequence (Genbank accession no. NC_092692) using BOWTIE.  The E. coli strain DH5α has an incomplete annotation and for this reason the E. coli K-12 annotation was used, representing an estimation of differentially expressed genes due to exposure of antimicrobials.  Mapped reads for 3 seperate sequencing runs were combined because some sequencing runs were not fully completed due to technical difficulties.  For each condition, graphs representing the number of mapped reads per nucleotide were generated and visualized using the Integrated Genome Viewer (IGV).  Images were created using XplasMap (http://www.iayork.com/XPlasMap/) and IGV.  The reads mapped per kilobase of gene per million (RPKM) reads was calculated using either the E. coli chromosome or the pAR060302 annotation and was used for global normalization.  The per kilobase cDNA length normalized the effect of different length of cDNAs such that the sequence reads have a equal chance to map on the long cDNA regions and the short cDNA regions.  After RPKM normalization, each sample is comparable to each other.  An R package, DEGseq , was used to identify differentially expressed genes between the control and each antibiotic treatment condition. PGCGROWTHCONDITIONS
SRR427120	GSE36248	GSM885047	GPL10328	PMID_	no treatment	Transcriptome mapping of blaCMY-2 positive IncA/C plasmid pAR060302	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	extract_protocol	Cells were pelleted and RNA was purified using a commercially available RNA extraction kit (Qiagen).  RNA preparations were then subjected to a DNase treatment to eliminate DNA contamination from the sample (Qiagen).  A treatment was also included to deplete ribosomal RNA using a commercially available kit (MicrobExpress, Ambion).  The two biological replicates for each growth condition were pooled for sequencing. PGCGROWTHCONDITIONS
SRR427120	GSE36248	GSM885047	GPL10328	PMID_	no treatment	Transcriptome mapping of blaCMY-2 positive IncA/C plasmid pAR060302	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	growth_protocol	E. coli strain DH5α harboring pAR060302 was grown in 10 mL DifcoTM Luria-Bertani (LB) broth aliquots at 37º C with shaking until an OD600 of 0.5. PGCGROWTHCONDITIONS
SRR427120	GSE36248	GSM885047	GPL10328	PMID_	no treatment	Transcriptome mapping of blaCMY-2 positive IncA/C plasmid pAR060302	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR427120	GSE36248	GSM885047	GPL10328	PMID_	no treatment	Transcriptome mapping of blaCMY-2 positive IncA/C plasmid pAR060302	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	source_name	bacteria grown at 37° C with shaking until log phase PGCGROWTHCONDITIONS
SRR427120	GSE36248	GSM885047	GPL10328	PMID_	no treatment	Transcriptome mapping of blaCMY-2 positive IncA/C plasmid pAR060302	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR427120	GSE36248	GSM885047	GPL10328	PMID_	no treatment	Transcriptome mapping of blaCMY-2 positive IncA/C plasmid pAR060302	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	strain: DH5α(pAR060302) PGCGROWTHCONDITIONS
SRR427120	GSE36248	GSM885047	GPL10328	PMID_	no treatment	Transcriptome mapping of blaCMY-2 positive IncA/C plasmid pAR060302	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	treatment: none PGCGROWTHCONDITIONS
SRR427120	GSE36248	GSM885047	GPL10328	PMID_	no treatment	Transcriptome mapping of blaCMY-2 positive IncA/C plasmid pAR060302	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	growth_protocol	E. coli strain DH5α harboring pAR060302 was grown in 10 mL DifcoTM Luria-Bertani (LB) broth aliquots at 37º C with shaking until an OD600 of 0.5. PGCGROWTHCONDITIONS
SRR427120	GSE36248	GSM885047	GPL10328	PMID_	no treatment	Transcriptome mapping of blaCMY-2 positive IncA/C plasmid pAR060302	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR427120	GSE36248	GSM885047	GPL10328	PMID_	no treatment	Transcriptome mapping of blaCMY-2 positive IncA/C plasmid pAR060302	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	source_name	bacteria grown at 37° C with shaking until log phase PGCGROWTHCONDITIONS
SRR427120	GSE36248	GSM885047	GPL10328	PMID_	no treatment	Transcriptome mapping of blaCMY-2 positive IncA/C plasmid pAR060302	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	contact_name	Timothy ,J.,Johnson PGCGROWTHCONDITIONS