SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	data_processing	Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	data_processing	FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	data_processing	Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	data_processing	Genome_build: NC_000913 PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	data_processing	Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	extract_protocol	Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen). PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	extract_protocol	Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming. PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	organism	Escherichia coli K-12 PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	source_name	cra KO PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	treatment_protocol	Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor[linebreak]s protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	genotype/variation: cra KO; BW25113 Dcra PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	growth stage: mid exponetial phase PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	oxygen condition: aerobic PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	supplementation: None PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	strain: K-12 PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	organism	Escherichia coli K-12 PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	source_name	cra KO PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	treatment_protocol	Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor[linebreak]s protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use. PGCGROWTHCONDITIONS
SRR922270	GSE48324	GSM1174833	GPL16227	PMID_24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	contact_name	Bernhard,O,Palsson PGCGROWTHCONDITIONS