"culture: 18 h at 37°C"	"characteristics_ch1.1"
"medium: LB"	"characteristics_ch1.2"
"symbioflor status: without Symbioflor"	"characteristics_ch1.3"
"conversion: Convert SOLiD output to fastq (Galaxy Version 1.0.0); default parameters."	"data_processing.1"
"mapping: bowtie (Galaxy Version 1.1.2); 28 nt seed length, maximal two mismatches in the seed, a maximal threshold of 70 for the sum of the quality values at mismatched positions."	"data_processing.2"
"counting: countOverlaps of Iranges; default parameters"	"data_processing.3"
"normalizing: convert counts in RPKM using Excel"	"data_processing.4"
"differential expression: Bioconductor package edgeR (version 3.2.3); default parameters"	"data_processing.5"
"Genome_build: NC_002655"	"data_processing.6"
"Supplementary_files_format_and_content: xlsx: logFC and p-value"	"data_processing.7"
"scraping bacteria, opening with bead beating, Trizol-based RNA isolation, rRNA depletion with RiboZero, DNA digest, SoLiD seq by CeGaT (Tübingen, Germany)"	"extract_protocol_ch1.1"
"conducted by CeGaT (Tübingen, Germany) according to SOLiD standard protocols for RNA-seq"	"extract_protocol_ch1.2"
"LB agar plates, 37°C for 18 h"	"growth_protocol_ch1.1"
"Escherichia coli O157:H7 str. EDL933"	"organism_ch1.1"
"without Symbioflor"	"source_name_ch1.1"
"EHEC"	"title.1"
"EHEC either grown on plain LB plates or LB plates containing Symbioflor within the agar"	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"culture: 18 h at 37°C"	"characteristics_ch1.1"
"medium: LB"	"characteristics_ch1.2"
"symbioflor status: without Symbioflor"	"characteristics_ch1.3"
"LB agar plates, 37°C for 18 h"	"growth_protocol_ch1.1"
"Escherichia coli O157:H7 str. EDL933"	"organism_ch1.1"
"without Symbioflor"	"source_name_ch1.1"
"EHEC either grown on plain LB plates or LB plates containing Symbioflor within the agar"	"treatment_protocol_ch1.1"