SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0 PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Genome_build: NC_000913 PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample. PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA). PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	ΔgadE pH5.5 PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	treatment_protocol	The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	strain: K-12 MG1655 PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: delta-gadE PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	ΔgadE pH5.5 PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	treatment_protocol	The cell culture was treated with the RNAprotect reagent (Qiagen). PGCGROWTHCONDITIONS
SRR1824560	GSE66481	GSM1623163	GPL16085	PMID_26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	contact_name	Donghyuk,,Kim PGCGROWTHCONDITIONS