"FastQ quality trimming using FastX (version 0.0.13)  and a cut-off value of 20"	"data_processing.1"
"Fastq to fasta conversion using FastX  FastX (version 0.0.13)"	"data_processing.2"
"5' linker and poly A-tail removal using READemption"	"data_processing.3"
"mapping of reads to E. coli O104:H4 rRNAs and tRNAs using READemption 0.3.7 and segemehl 0.2.0"	"data_processing.4"
"mapping of non-rRNA and tRNA reads to E. coli O104:H4 chromosome and plasmids using READemption 0.3.7 and segemehl 0.2.0"	"data_processing.5"
"generation of coverage graphs representing the number of pAA plasmid-associated mapped reads per nucleotide using READemption 0.3.7"	"data_processing.6"
"normalization of graphs to the total number of mapped reads per library using READemption 0.3.7"	"data_processing.7"
"Genome_build: NC_018658.1, NC_018659.1, NC_018660.1, NC_018666.1"	"data_processing.8"
"Supplementary_files_format_and_content: wig files representing the normalized number of pAA-associated mapped reads per nucleotide. Files contain wiggle-formatted files data for accessions  NC_018658.1, NC_018659.1, NC_018660.1, and NC_018666.1."	"data_processing.9"
"Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of 1U/L RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). Next, the sample (TEX+) was depleted of processed RNAs using 1U per 1μg of RNA Terminator 5´-Phosphate-Dependent Exonuclease (TEX, Epicentre) in the presence of 1U/μL RNase Inhibitor for 60 min at 30° C. A control reaction without TEX (TEX-) was run in parallel. Following organic extraction, RNA was recovered by overnight precipitation and resuspended in RNase-free water."	"extract_protocol_ch1.1"
"cDNA libraries for the Illumina sequencing platform were constructed by vertis Biotechnology AG, Germany, as described previously (Berezikov et al.,2006), without the RNA size-fractionation step prior to cDNA synthesis. Briefly, RNA samples were polyA-tailed using polyA polymerase. Then, the 5'-PPP termini were converted to 5'-P using tobacco acid pyrophosphatase (TAP) to allow for the ligation of the 5’ end RNA adapter. First-strand cDNA was synthesized by an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. In a PCR-based amplification step using a high fidelity DNA polymerase the cDNA concentration was increased to 20-30 ng/µl. A library-specific barcode for multiplex sequencing was part of a 3'-sequencing adapter."	"extract_protocol_ch1.2"
"An overnight culture of E. coli O104:H4 strain LB226692 was diluted 1:10,000 in pre-warmed LB medium (10 g/L tryptone, 5 g/L yeast extract, 5 g/L NaCl) and cells were grown at 37oC, 180 rpm for 3.5 h to an OD600 of 0.52."	"growth_protocol_ch1.1"
"Escherichia coli O104:H4"	"organism_ch1.1"
"exponentially growing cells"	"source_name_ch1.1"
"TEX+_E. coli O104:H4"	"title.1"
"5 ml of cell suspension were added to 0.625 ml of pre-chilled stop solution (5 % phenol/95 % ethanol), vortexed and incubated for 5 min on ice. Cells were pelleted for 5 min at 5000 g, flash frozen in a dry ice-ethanol bath and stored at -80oC."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"strain: clinical isolate LB226692"	"characteristics_ch1.1"
"origin of isolation: patient with hemolytic uremic syndrome (HUS)"	"characteristics_ch1.2"
"outbreak: 2011 outbreak centered in Northern Germany"	"characteristics_ch1.3"
"An overnight culture of E. coli O104:H4 strain LB226692 was diluted 1:10,000 in pre-warmed LB medium (10 g/L tryptone, 5 g/L yeast extract, 5 g/L NaCl) and cells were grown at 37oC, 180 rpm for 3.5 h to an OD600 of 0.52."	"growth_protocol_ch1.1"
"Escherichia coli O104:H4"	"organism_ch1.1"
"exponentially growing cells"	"source_name_ch1.1"
"5 ml of cell suspension were added to 0.625 ml of pre-chilled stop solution (5 % phenol/95 % ethanol), vortexed and incubated for 5 min on ice. Cells were pelleted for 5 min at 5000 g, flash frozen in a dry ice-ethanol bath and stored at -80oC."	"treatment_protocol_ch1.1"