SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Sequencing reads (approximately 13 to 25 million per sample) were imported into Geneious Pro (Biomatters) and assembled to the reference chromosome MG1655 (GenBank Accession Number 000913.2). The assembly process was set to medium/low sensitivity on Geneious, with the following parameters: 10% gaps allowed per read; word length of 18; index word length of 13; words repeated more than 12 times ignored; 20% maximum mismatches per read; and maximum ambiguity of 4 PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Read coverage maps and RPKM data was subsequently generated by Geneious. PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	BAM files of the resulting assembly data were exported to JMP Genomics (SAS).  TMM normalization and ANOVA analysis of the read samples were conducted in JMP Genomics PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB. PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	MG1655 PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	treatment_protocol	MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour. PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	genotype: Wildtype PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB. PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	MG1655 PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	treatment_protocol	MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour. PGCGROWTHCONDITIONS
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548	PMID_	MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	contact_name	Rachel,,Krasich PGCGROWTHCONDITIONS