SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	The bcl2fastq Conversion Software v. 1.8.4 from Illumina (http://support.illumina.com/downloads.html) was used to translate cluster intensity values into fastq files. PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Sequenced reads were trimmed for adaptor sequence using Cutadapt v. 1.8.3, then mapped to E. coli K12 substr. W3110 whole genome from NCBI (GenBank: AP009048.1) using the RNA-seq aligner STAR v.2.4.2a. PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Raw counts were derived for each gene based on the respective annotations available from UCSC genome browser (http://genome.ucsc.edu) for the chosen reference sequence applying HTseq-count v. 0.6.1 in the intersection-nonempty mode. PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	HTseq-derived raw count data were used as input after a non-specific filtering step that removed residual rRNAs and tRNAs  and low coverage genes with fewer than 2 counts per million (16-20 reads) in more than 25% of the dataset. PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Genome_build: ASM1024v1 (NCBI E. coli K12 subst. W3110 genome (GenBank: AP009048.1)) PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: xlsx file format includes raw gene counts for each sample before and after filtering for low coverage genes PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	extract_protocol	The RNeasy mini kit, with on column RNase-Free DNase I treatment, (both Qiagen, Hilden, Germany) was used for total RNA isolation (RNA ≥ 200 bases), according to the manufacturer’s protocol. RNA quality was determined by a Lab-on-a-Chip-System Bioanalyzer 2100 (Agilent, Boeblingen, Germany). PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	extract_protocol	First, ribosomal RNA was depleted from 1 μg of total RNA using the Ribo-ZeroTM Magnetic Kit (Bacteria) (Epicentre, Madison, WI, USA). Next, mRNA libraries were prepared using the TruSeq mRNA Library Prep Kit (Illumina, San Diego, CA, USA). mRNA libraries were prepared for sequencing using standard Illumina protocols. PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	source_name	chemostat STR-PFR culture PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	treatment_protocol	Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	strain: K12 W3110 PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	sample port: PFR P3 PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	time: 120min PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	replicate: 1 PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	source_name	chemostat STR-PFR culture PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	treatment_protocol	Sampling by directly placing the culture sample into RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), following short centrifugation the pellet was stored at −70°C. PGCGROWTHCONDITIONS
SRR5071610	GSE90743	GSM2411690	GPL18133	PMID_28447391PMID_28702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	contact_name	Joana,Danica,Simen PGCGROWTHCONDITIONS