"genoype: Wild-Type"	"characteristics_ch1.1"
"phenotype: normal"	"characteristics_ch1.2"
"growth condition: anaerobic"	"characteristics_ch1.3"
"strain: K-12"	"characteristics_ch1.4"
"Resulting reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software package SOAP (Li et al, 2009), allowing no more than two mismatches (Supplemental File).  Reads aligning to repeated elements in the genome (e.g. rRNA) were removed from analysis.  For reads that had no mapping locations for the first 36 bp, the 3-30 bp subsequences were used in the subsequent mapping to the reference genome.  Reads that had unique mapping locations and did not match annotated rRNA genes were used for further analysis.  For each gene, the tag density was estimated as the number of aligned sequencing tags divided by gene size in kb.  Per-gene tag density was normalized using quantile normalization (Supplemental Files).  The tag density data were analyzed for statistically significant differential expression using BaySeq (Hardcastle & Kelly, 2010) with a FDR of 0.01, and genes were organized into operons using data from EcoCyc (Keseler et al, 2011)."	"data_processing.1"
"Genome Build:"	"data_processing.2"
"WT_Anaerobic_RNAseq_A_Tag_Count.txt: U00096.2"	"data_processing.3"
"WT_Anaerobic_RNAseq_A_WIG.wig: U00096.2"	"data_processing.4"
"The RNAs were chemically fragmented using RNA Fragmentation Reagents (Ambion) to the size range of 200-250 bp using 1x fragmentation solution for 5 minutes at 70°C (Ambion).  Double stranded cDNA was generated using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) following the manufacturer’s protocol.  The Illumina Paired End Sample Prep kit was used for Illumina RNA-seq library creation using the manufacturer’s instructions.  Briefly, the fragmented cDNA was end repaired, ligated to Illumina specific adapters and amplified with 10 cycles of PCR using the TruSeq SR Cluster Kit (v2).  Single-end 36 bp reads were generated by sequencing on the Illumina Genome Analyzer IIx, using the TruSeq SBS Kit (v5) following the manufacturer’s protocol."	"extract_protocol_ch1.1"
"Escherichia coli MG1655 K-12 WT and ∆fnr were grown to mid-log phase (O.D.600nm 0.3) anerobically (95% N2, 5% CO2) at 37°C in MOPS +0.2% glucose media (Ref)."	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655star"	"organism_ch1.1"
"Escherichia coli MG1655 K-12 WT"	"source_name_ch1.1"
"Ecoli_wild-type_rep1_anaerobic"	"title.1"
"Cells were treated with a stop solution of Phenol and Ethanol, spun down and flash frozen and stored at -80°C (ref). Total RNA was extracted using a hot phenol method (ref). RNA quality was determined by analysis with an Agilent 2100 bioanalyzer and quantity was determined using a NanoDrop. To enrich for mRNA, the 23S and 16S rRNA were removed using the Ambion MICROBExpress kit (Ambion) following manufacturer’s guidelines, except the total RNA was incubated with the rRNA oligonucleotides for one hour instead of 15 minutes."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"genoype: Wild-Type"	"characteristics_ch1.1"
"phenotype: normal"	"characteristics_ch1.2"
"growth condition: anaerobic"	"characteristics_ch1.3"
"strain: K-12"	"characteristics_ch1.4"
"Escherichia coli MG1655 K-12 WT and ∆fnr were grown to mid-log phase (O.D.600nm 0.3) anerobically (95% N2, 5% CO2) at 37°C in MOPS +0.2% glucose media (Ref)."	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655star"	"organism_ch1.1"
"Escherichia coli MG1655 K-12 WT"	"source_name_ch1.1"
"Cells were treated with a stop solution of Phenol and Ethanol, spun down and flash frozen and stored at -80°C (ref). Total RNA was extracted using a hot phenol method (ref). RNA quality was determined by analysis with an Agilent 2100 bioanalyzer and quantity was determined using a NanoDrop. To enrich for mRNA, the 23S and 16S rRNA were removed using the Ambion MICROBExpress kit (Ambion) following manufacturer’s guidelines, except the total RNA was incubated with the rRNA oligonucleotides for one hour instead of 15 minutes."	"treatment_protocol_ch1.1"