"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."	"data_processing.1"
"Genome Build:"	"data_processing.2"
"Ampicilin_treatment_plasmidmappedreads_statistical_output.txt: NC_012692.1"	"data_processing.3"
"Amp_Treatment_genomemappedreads_statistical_output.txt: NC_000913.2"	"data_processing.4"
"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."	"extract_protocol_ch1.1"
"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."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"bacteria grown at 37° C with shaking until log phase with ampicilin treatment"	"source_name_ch1.1"
"ampicilin treatment"	"title.1"
"RNA-Seq"	"library_strategy.1"
"strain: DH5α(pAR060302)"	"characteristics_ch1.1"
"treatment: ampicillin (50 µg/mL final concentration)"	"characteristics_ch1.2"
"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."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"bacteria grown at 37° C with shaking until log phase with ampicilin treatment"	"source_name_ch1.1"