"The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing"	"data_processing.1"
"bowtie2 v2.2.3 was used for alignment"	"data_processing.2"
"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)."	"data_processing.3"
"Genome_build: NC_000913.2"	"data_processing.4"
"Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format"	"data_processing.5"
"Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit."	"extract_protocol_ch1.1"
"rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies)."	"extract_protocol_ch1.2"
"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."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"E. coli K12 MG1655"	"source_name_ch1.1"
"RNAseq_delta-crp_fructose_NH4Cl_O2_2"	"title.1"
"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."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"strain: delta Crp"	"characteristics_ch1.1"
"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."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"E. coli K12 MG1655"	"source_name_ch1.1"
"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."	"treatment_protocol_ch1.1"