SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	bowtie2 v2.2.3 was used for alignment PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013). PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Genome_build: NC_000913.2 PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	data_processing	Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit. PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies). PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	E. coli K12 MG1655 PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	treatment_protocol	Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	strain: delta Crp PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample. PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	E. coli K12 MG1655 PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	treatment_protocol	Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010).  Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment. PGCGROWTHCONDITIONS
SRR1751328SRR1751329	GSE64848	GSM1581594	GPL16085	PMID_29771928	RNAseq_delta-crp_glucose_NH4Cl_O2_3	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GPL16085: Illumina MiSeq (Escherichia coli)	contact_name	Haythem,,Latif PGCGROWTHCONDITIONS