"Illumina GAII reads were filtered by SGA version 0.9.9 with the following options: sga preprocess -q 10 -f 10 -m 25 (quality trim 10, quality filter 10, minimal length 25)"	"data_processing.1"
"preprocessed RNA-Seq reads were mapped to the reference Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) by BWA toolkit version 0.5.9-r16 with the following options: bwa aln -q 20"	"data_processing.2"
"Differentially expressed genes were identified by processing raw counts of mapped reads with edgeR R library version 2.6.9. Normalized counts for each biological replicate were averaged between two technical replicates."	"data_processing.3"
"Differentially expressed (DE) genes in all stress evolved strains were found relative to the expression levels in the reference G500 strain using the edgeR R package."	"data_processing.4"
"Genes with BH (Benjamini and Hochberg) adjusted p-values below 0.05 threshold were selected as DE genes."	"data_processing.5"
"Genes from the amplified regions in O500 (12-fold) and P500 (two-fold) strains are significantly over-expressed relative to the reference: average log Fold Change for concentrations is +3.6 and +0.8 (both with p-values<10-20), respectively."	"data_processing.6"
"Genome_build: Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2)"	"data_processing.7"
"Supplementary_files_format_and_content: Tab delimited text file; includes: gene differential expression levels relative to the G500 strain with corresponding p-values and processed counts for each biological replicate (each normolized and averaged between 2 technical replicates).  Linked as supplementary file on Series record."	"data_processing.8"
"RNA was extracted using an RNeasy kit (Qiagen) and after 1st and 2nd strand cDNA synthesis, linker ligation and size selection subjected to shotgun sequencing using single read 40bp read length runs on an Illumina Genome Analyzer GAII."	"extract_protocol_ch1.1"
"Clones were grown in M9 with 0.4% (w/v) glucose as carbon source minimal medium with 0.3M NaCl (osmotic stress medium) to mid-log phase (OD600 approx. 0.8)."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Bacterial cell"	"source_name_ch1.1"
"B500_1"	"title.1"
"1mL aliquots were harvested and mixed with 0.5mL Phenol/ethanol (5% (v/v) Phenol in EtOHabs). Cells were collected by centrifugation and stored at -80°C until use."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"strain: MG 1655"	"characteristics_ch1.1"
"stress: n-butanol"	"characteristics_ch1.2"
"biological replicate: 1"	"characteristics_ch1.3"
"technical replicates: 2"	"characteristics_ch1.4"
"Clones were grown in M9 with 0.4% (w/v) glucose as carbon source minimal medium with 0.3M NaCl (osmotic stress medium) to mid-log phase (OD600 approx. 0.8)."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"Bacterial cell"	"source_name_ch1.1"
"1mL aliquots were harvested and mixed with 0.5mL Phenol/ethanol (5% (v/v) Phenol in EtOHabs). Cells were collected by centrifugation and stored at -80°C until use."	"treatment_protocol_ch1.1"