"Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina)."	"data_processing.1"
"The sequence data were mapped against the genome sequence of E. coli K12 substr. MG1655 (NCBI accession number NC_000913.3) using Bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923)."	"data_processing.2"
"Gene expression was calculated as reads per gene by determining the number of reads that overlapped with the annotated gene loci using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'."	"data_processing.3"
"Genome_build: NC_000913.3 E. coli K12 substr. MG1655"	"data_processing.4"
"Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of NC_000913.3 available from NCBI."	"data_processing.5"
"Total RNA was isolated with the RNeasy Protect Bacteria Mini Kit from Qiagen (Hilden, Germany). The isolated RNA was further purified from genomic DNA contaminations using Ambion DNase I treatment following the manufacturer's instructions (DNA-free, Ambion by Life Technologies, Darmstadt, Germany). RNA samples were further subjected to an mRNA enrichment step using the MICROBExpress Kit from Ambion according to the manufacturer`s instructions (Life Technologies, Darmstadt, Germany)."	"extract_protocol_ch1.1"
"Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al. 2009). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane. Sequencing was performed on a HiSeq1500 using SBS v3 kits (Illumina) to generate paired-end reads of 2 x 50 nucleotides."	"extract_protocol_ch1.2"
"Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions."	"growth_protocol_ch1.1"
"Escherichia coli K-12"	"organism_ch1.1"
"delta-rnr mutant_oxic_glycerol"	"source_name_ch1.1"
"d_rnr O2 1"	"title.1"
"No further treatment was applied."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"genotype/variation: K-12 delta-rnr mutant (JW5741-1)"	"characteristics_ch1.1"
"oxic/anoxic: oxic"	"characteristics_ch1.2"
"carbon source: glycerol"	"characteristics_ch1.3"
"molecule subtype: total RNA (ribosome-depleted)"	"characteristics_ch1.4"
"Cells were grown at 37°C in M4 minimal medium under oxic and anoxic conditions. The minimal medium (1.27 mM K2HPO4, 0.73 mM KH2PO4, 5 mM sodium HEPES, 150 mM NaCl, 9 mM (NH4)2SO4) was supplemented with 0.1 g/l caseinhydrolysate 1 mM MgSO4, 0.1 mM CaCl2 and trace elements (5 μM CoCl2, 0.2 μM CuSO4, 57 μM H3BO3, 5.4 μM FeCl2, 1.3 μM MnSO4, 67.2 μM Na2EDTA, 3.9 μM Na2MoO4, 1.5 μM Na2SeO4, 5 μM NiCl2, and 1 μM ZnSO4). The pH of the media was adjusted to 7.2. Glycerol (50 mM) or glycerol (50mM) plus propionate (10 mM) served as the carbon and electron sources, respectively. Potassium nitrate (50 mM) was the electron acceptor under anoxic conditions."	"growth_protocol_ch1.1"
"Escherichia coli K-12"	"organism_ch1.1"
"delta-rnr mutant_oxic_glycerol"	"source_name_ch1.1"
"No further treatment was applied."	"treatment_protocol_ch1.1"