"genotype/variation: galT mutant"	"characteristics_ch1.1"
"The program used to generate the bed/bar files is “Affymetrix Tiling Analysis Software.” Standardized signals, for each probe in the arrays, were generated using the MAT software (Johnson WE et al. 2006), which provides a model-based, sequence-specific, background correction for each sample. A gene-specific score was then calculated for each gene by averaging all MAT scores (natural log) for all probes under the annotated gene coordinates. Gene annotation was from the ASAP database (Glasner JD et al. 2003) at the University of Wisconsin-Madison, for E. coli K-12 MG1655 version m56. Differences of two log scale values in the absence or presence of D-galactose were calculated in galT mutant cells.  Finally, the transcriptome results (log scale values) with or without D-galactose were compared graphically [References: Johnson WE, et al. (2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci USA 103:12457–12462; Glasner JD, et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res 31:147–151]"	"data_processing.1"
"The TAS software provides analysis capabilities specifically for the GeneChip® Tiling Arrays. TAS analyzes feature intensity data stored in GCOS output .CEL files and produces:"	"data_processing.2"
"Signal and p-values for each genomic position interrogated."	"data_processing.3"
"Computation of genomic intervals based on computed signal and p-values"	"data_processing.4"
"Computation of summary statistics"	"data_processing.5"
"Visualizations for assessing the quality of the array data"	"data_processing.6"
"Cells were then placed on ice and RNAprotect™ bacteria reagent (Qiagen) was added to stabilize the RNA. Total RNAs of cells were purified by RNeasy mini kit (Qiagen). Isolated RNA (10 ug) was used for random primer cDNA synthesis using SuperScript II reverse transcriptase, 18064–071 (Invitrogen). The reaction mixture was then subsequently treated with 1 N NaOH to degrade any remaining RNA and treated with 1 N HCl to neutralize the NaOH. Synthesized cDNA was then purified using MiniElute PCR purification columns, 28004 (Qiagen). Purified cDNA (3 ug) was fragmented to between 50 and 200 bps by 0.6 U/ g of DNase I, 27–0514-01 (Amersham Biosciences) for 10 min at 37 °C in 1  One-Phor-All buffer, 27–0901-02 (Amersham Biosciences). Heat inactivation of the DNase I enzyme was performed at 98 °C for 10 min."	"extract_protocol_ch1.1"
"E. coli galT mutant cells were cultivated in 125-mL corning flasks containing 30 mL of M63 minimal medium plus glycerol (final 0.3%) at 37 °C."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"with D-galactose"	"source_name_ch1.1"
"E. coli galT mutant with galactose"	"title.1"
"At OD600 of 0.5, cell cultures were separated into two flasks. D-galactose (final 0.3%) was added to one and cells were grown for 1.5 h further."	"treatment_protocol_ch1.1"
"genotype/variation: galT mutant"	"characteristics_ch1.1"
"E. coli galT mutant cells were cultivated in 125-mL corning flasks containing 30 mL of M63 minimal medium plus glycerol (final 0.3%) at 37 °C."	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"with D-galactose"	"source_name_ch1.1"
"At OD600 of 0.5, cell cultures were separated into two flasks. D-galactose (final 0.3%) was added to one and cells were grown for 1.5 h further."	"treatment_protocol_ch1.1"