"sample type: cDNA produced by RT of RNA deriving from vitro transcription, with RNA polymerase E σS, of 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI"	"characteristics_ch1.1"
"After quality controls of data distribution the raw data (CEL files) were used to perform, normalization and probe set summarization through RMA algorithm (Robust Multiarray Analysis) by using the Affymetrix Gene Expression Console Software (www.affymetrix.com).   Normalized data were then uploaded into OneChannelGUI Software (http://www.bioinformatica.unito.it/oneChannelGUI/)  to perform a differential expression analysis. As the dataset is limited in number of samples and replicates (4 GeneChips hybridized, 2 replicates for each condition) we decided to apply a  simple non-parametric statistical method based on ranks of fold changes to perform a two-class paired differential analysis. To select only significatively differentially expressed genes we set the following parameters for the Rank Product analysis: 100 permutations and 0.1 cut-off percentage of false positives (pfp) which corresponds to a p-value<0.01."	"data_processing.1"
"E. coli RNA polymerase core enzyme was purchased from Epicentre (Madison, WI, USA). Histidine-tagged σ factors were produced and purified as described (Lacour et al., 2003; Checroun et al., 2004); proteins appeared pure from contaminants as determined by denaturing protein gel electrophoresis (data not shown). For reconstitution of RNA polymerase holoenzymes, the core enzyme was incubated for 10 minutes at 37 °C with either σS or σ70 at a 1:10 ratio. For calculation of RNA polymerase concentrations in transcription assays, it was assumed that, after reconstitution, core enzyme would be 100% active and fully saturated by either σ factor. 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI were used in transcription assays for ROMA experiments. RNA polymerase holoenzyme concentrations were 100 nM in 50 ul reaction mixture. Ten independent run-off transcription assays were performed, and transcripts were pooled together (ca. 1 ug total RNA)."	"extract_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"RNA produced by in vitro transcription, with RNA polymerase E σS, of 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI"	"source_name_ch1.1"
"E.coli_IVT-RNA_sigmaS"	"title.1"
"sample type: cDNA produced by RT of RNA deriving from vitro transcription, with RNA polymerase E σS, of 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI"	"characteristics_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"RNA produced by in vitro transcription, with RNA polymerase E σS, of 2 ug of genomic DNA from E. coli MG1655 digested with EcoRI"	"source_name_ch1.1"