SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	data_processing	For RNA-Seq analysis, the fastq file produced from the machine was demultiplexed into a separate file for each sample. PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	data_processing	Index sequences accompanying with reads were compared with pre-designed barcodes, allowing two base mismatches at most. PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	data_processing	The low-quality of raw reads were trimmed using Trimmomatic (v0.30) with default settings. PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	data_processing	Trimmed reads were aligned on most recent reference genome of Escherichia coli (GenBank U00096.3) by using TopHat (v2.0.10) coupled with bowtie (v1.0.0). PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	data_processing	HTSeq is used to generate expression count for each gene. PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	data_processing	Genome_build: RefSeq NC_000913.3 PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	data_processing	Supplementary_files_format_and_content: htcount : expression count for each gene and its name. PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	extract_protocol	Bacteria were harvested with 0.5 Vol of 5% phenol in ethanol and frozen at -80C. Total RNA was extracted from frozen cultures using RNeasy kit (Qiagen). PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	extract_protocol	Library constructed using KAPA Kit. PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	organism	Escherichia coli BW25113 PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, WT, M9 and 0.3% glucose PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	strain/background: BW25113 PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	media: M9 PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	organism	Escherichia coli BW25113 PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, WT, M9 and 0.3% glucose PGCGROWTHCONDITIONS
SRR2547488	GSE73672	GSM1900491	GPL20227	PMID_27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	contact_name	Ilias,,Tagkopoulos PGCGROWTHCONDITIONS