"strain: MG1655"	"characteristics_ch1.1"
"We developed in-house computational and statistical analysis tools for use with the E. coli tiling array.  We used a previous study (Choe et al., 2005) as a model for perfect match adjustment on single arrays.  Analysis scripts were written in Perl, MatLab, and R to standardize the statistical manipulations across all data sets. The output file from the scanning process is a CEL file. The raw CEL data were used as the basis for the manuscript; no processed data are available."	"data_processing.1"
"Genomic DNA Extraction: Genomic DNA was extracted according to Current Protocols in Molecular Biology.  Protein-DNA complex isolation: Protein-DNA complexes were isolated by phenol extraction with 150 μL 10 mM Tris and 500 μL 25:24:1 phenol : chloroform : isoamyl alcohol.  A white disk was readily discernible at the aqueous/organic interface. To purify this interface, all aqueous and organic liquid was removed by pipetting. A second extraction was performed by adding 500 μL 10 mM Tris and 450 μL 24:1 chloroform: isoamyl alcohol, vortexing and centrifuging.  Again, all liquid was removed from the interface by pipetting, and residual liquid was removed. For cross-link reversal: the interface was suspended in 500 μL 10 mM Tris and 50 μL 10% SDS, and placed at ~100 ˚C for 30 minutes. The tubes were placed on ice, then moved to 65 ˚C for 3 hours following addition of 5 μL proteinase K (20 mg/mL). After heat treatment, the solutions were phenol/chloroform extracted and ethanol precipitated in the presence of glycogen to purify the DNA.  RNA extraction: the Qiagen RNeasy kit (P/N 74104) was used to isolate total cellular RNA. Immediately following elution in RNase-free water, residual DNA was removed by treatment with DNaseI at 37 °C for 15 minutes. The samples were treated again using the RNeasy kit, resuspended in 40 μl RNase-free water, and stored at -20 °C."	"extract_protocol_ch1.1"
"Batch cultures of E. coli MG1655 were grown at 37°C with shaking in Luria-Bertani medium (0.1% Bacto Tryptone, 0.05% yeast extract, 0.05% NaCl)."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"MG1655 genomic DNA"	"source_name_ch1.1"
"genomic_ref5"	"title.1"
"For cross-linking, 30 mL of cells were mixed with 300 uL 1M sodium phosphates (pH 7.6) and 810 uL 37% formaldehyde. Cross-linking was quenched by addition of 2 mL 2M glycine. Protein-DNA complexes were isolated from cells grown to early (2.4 x 10^7 CFU/ml) or late (2.4 x 10^8 CFU/ml) exponential phase.  Batch cultures of E. coli MDS42 were grown to early exponential phase.  To obtain tiling-resolution RNA measures across the E. coli genome, wild-type cells were grown in biological duplicate in LB to early exponential phase. The cultures were moved to ice, and the Qiagen RNeasy kit (P/N 74104) was used to isolate total cellular RNA."	"treatment_protocol_ch1.1"
"strain: MG1655"	"characteristics_ch1.1"
"Batch cultures of E. coli MG1655 were grown at 37°C with shaking in Luria-Bertani medium (0.1% Bacto Tryptone, 0.05% yeast extract, 0.05% NaCl)."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"MG1655 genomic DNA"	"source_name_ch1.1"
"For cross-linking, 30 mL of cells were mixed with 300 uL 1M sodium phosphates (pH 7.6) and 810 uL 37% formaldehyde. Cross-linking was quenched by addition of 2 mL 2M glycine. Protein-DNA complexes were isolated from cells grown to early (2.4 x 10^7 CFU/ml) or late (2.4 x 10^8 CFU/ml) exponential phase.  Batch cultures of E. coli MDS42 were grown to early exponential phase.  To obtain tiling-resolution RNA measures across the E. coli genome, wild-type cells were grown in biological duplicate in LB to early exponential phase. The cultures were moved to ice, and the Qiagen RNeasy kit (P/N 74104) was used to isolate total cellular RNA."	"treatment_protocol_ch1.1"