"strain: E. coli K12 MG1655"	"characteristics_ch1.1"
"strain: Human sewage isolate H2"	"characteristics_ch2.1"
"Images were analyzed using a combination of GenePix Pro 6.0, the freely available TIGR TM4 software suite (www.tm4.org ) and Microsoft Excel.  Spots with an intensity: background ratio > 1.5 and overall intensity > 350 in the reference channel and an intensity:background ratio of > 1.0 in the experimental channel were considered acceptable for downstream processing.  Local background was subtracted for each spot, the corresponding log2 ratios were normalized using total intensity normalization, and replicate spots were averaged using TIGR MIDAS.  Genes that had missing data (i.e. unacceptable spots) for more than one-third of the samples were excluded from the downstream analysis leaving 3993 ORFs in the final data set.  Each sample was hybridized twice and the results averaged in Microsoft Excel after processing with MIDAS.  A strict cutoff of log2 ratio > 0.9 or < 0.9 was applied for the determination of gene amplifications and gene absences, respectively."	"data_processing.1"
"Genomic DNA was extracted using an SDS lysis/phenol/chloroform method described by (Syn CK, Swarup S (2000) A scalable protocol for the isolation of large-sized genomic DNA within an hour from several bacteria. Anal Biochem 278: 86-90) with slight modifications as follows:  subsequent to DNA precipitation, spun pellets were treated with 50μg mL-1 DNAse-free RNAse A and incubated at 37°C for 30 min.  Samples were then re-extracted once with phenol:chloroform (3:1), once with phenol:chloroform (1:1), twice with chloroform, reprecipitated and then resuspended in TE, pH 8.0."	"extract_protocol_ch1.1"
"Genomic DNA was extracted using an SDS lysis/phenol/chloroform method described by (Syn CK, Swarup S (2000) A scalable protocol for the isolation of large-sized genomic DNA within an hour from several bacteria. Anal Biochem 278: 86-90) with slight modifications as follows:  subsequent to DNA precipitation, spun pellets were treated with 50μg mL-1 DNAse-free RNAse A and incubated at 37°C for 30 min.  Samples were then re-extracted once with phenol:chloroform (3:1), once with phenol:chloroform (1:1), twice with chloroform, reprecipitated and then resuspended in TE, pH 8.0."	"extract_protocol_ch2.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"E. coli K12 MG1655"	"source_name_ch1.1"
"Human sewage isolate H2"	"source_name_ch2.1"
"Human II versus MG1655 technical replicate 2"	"title.1"
"strain: E. coli K12 MG1655"	"characteristics_ch1.1"
"strain: Human sewage isolate H2"	"characteristics_ch2.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"E. coli K12 MG1655"	"source_name_ch1.1"
"Human sewage isolate H2"	"source_name_ch2.1"