SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	data_processing	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) PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	data_processing	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 PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	data_processing	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. PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	data_processing	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. PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	data_processing	Genes with BH (Benjamini and Hochberg) adjusted p-values below 0.05 threshold were selected as DE genes. PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	data_processing	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. PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	data_processing	Genome_build: Escherichia coli strain K12 sub-strain MG1655 genome (GenBank accession no. U00096.2) PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	data_processing	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. PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	extract_protocol	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. PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	growth_protocol	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). PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	source_name	Bacterial cell PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	treatment_protocol	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. PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	strain: MG 1655 PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	stress: acidic PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	biological replicate: 1 PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	technical replicates: 2 PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	growth_protocol	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). PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	source_name	Bacterial cell PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	treatment_protocol	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. PGCGROWTHCONDITIONS
SRR534278	GSE39926	GSM981544	GPL10328	PMID_23385483	P500_1	Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	contact_name	Vadim,,Mozhayskiy PGCGROWTHCONDITIONS