SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	data_processing	We use Rockhopper for alignment and the complete analysis of data PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	data_processing	Genome_build: NC_018220 and NC_000913 PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	data_processing	Supplementary_files_format_and_content: tab-delimited text files include the average of the expression values obtained in Rockhopper for the replicates of each condition PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	data_processing	Supplementary_files_format_and_content: T1E_LB.xlsx: Average of expression values of samples DOT-T1E_LB1 and LB2 PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	data_processing	Supplementary_files_format_and_content: CoT1E_LB.xlsx: Average expression values of reads related with DOT-T1E strain in samples Co-culture_LB1 and LB2 PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	data_processing	Supplementary_files_format_and_content: K12_LB.xlsx: Average of expression values of samples MG1655_LB1 and LB2 PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	data_processing	Supplementary_files_format_and_content: CoK12_LB.xlsx: Average expression values of reads related with MG1655 strain in samples Co-culture_LB1 and LB2 PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	extract_protocol	Single colonies of P. putida strain DOT-T1E and E. coli MG1655 were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 50 ml aliquots were disposed in separate 250 ml Erlenmeyer flasks and incubated with shaking at 200 rpm. When cultures reached exponential phase (0.5 at OD600), antibiotics were added at sub-lethal concentrations to the culture medium to reach a final concentration of 1 µg/ml kanamycin, 300 µg/ml ampicillin, 150 µg/ml chloramphenicol, 4 µg/ml tetracycline, 0.5 µg/ml ciprofloxacin, 300 µg/ml spectinomycin, 500 µg/ml rifampicin and 2 µg/ml gentamicin. Then cultures were incubated under the same conditions for one hour more. Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution (95% (v/v) ethanol, 5% (v/v) phenol) and pelleted by centrifugation. After that, total RNA was extracted with Trizol (Invitrogen). Removal of DNA was carried out by treatment with DNase I (Fermentas) in combination with the RNase inhibitor RiboLock (Fermentas). The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	extract_protocol	RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	source_name	MG1655_LB PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	characteristics	strain: MG1655 PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	source_name	MG1655_LB PGCGROWTHCONDITIONS
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101	PMID_	MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	contact_name	Carlos,Molina,Santiago PGCGROWTHCONDITIONS