"strain: PC1012"	"characteristics_ch1.1"
"tissue source: kidney from CD-1 mice"	"characteristics_ch1.2"
"The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100."	"data_processing.1"
"Infected kidney solutions were centrifuged at 5000xg for 10 min to separate bacteria (pellet) from kidney (surface of RNA-later solution) cells.  The kidney cells were evacuated from the top of the solution, and the remaining solution was spun once more at 12000xg for 10 min, followed by disposal of the supernatant.  Pelleted cells were resuspended in TE buffer and treated with lysozyme (Sigma) at 1mg/ml final concentration for 5 min, and samples of 3-5 infected mice were pooled together for each infection group.  Nucleic acids were extracted via the RNA extraction protocol and products of the RNAeasy kit (Qiagen).  Following column purification, RNA samples were treated with DNAse Turbo (Ambion) for 30 min at 37C, followed by quantification of RNA using a spectrophotometer.  Remaining polyadenylated eukaryotic RNA was depleted from the samples following the MicroEnrich (Ambion) protocol and resuspended in 20l of TE buffer.  RNA was quantified spectrophotometrically and equal amounts (~300-500ng) of KMD and PC1012 RNA samples were subjected to the MessageAmp (Ambion) RNA amplification protocol.  Resultant amplified RNA was quantified and equal amounts were used in the Affymetrix protocol for prokaryotic cDNA synthesis and biotin labeling."	"extract_protocol_ch1.1"
"Bacteria were inoculated by direct injection of the mouse bladder, and kidney samples were taken at day 2 post-infection"	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"cDNA made from strain PC1012(marArobsoxS) extracted from mouse kidney on day 2 post infection"	"source_name_ch1.1"
"PC 2"	"title.1"
"Mouse kidneys were homogonized in RNALater solution (Ambion) and bacterial titers were taken.  Samples were pooled, and centrifuged as described below"	"treatment_protocol_ch1.1"
"strain: PC1012"	"characteristics_ch1.1"
"tissue source: kidney from CD-1 mice"	"characteristics_ch1.2"
"Bacteria were inoculated by direct injection of the mouse bladder, and kidney samples were taken at day 2 post-infection"	"growth_protocol_ch1.1"
"Escherichia coli"	"organism_ch1.1"
"cDNA made from strain PC1012(marArobsoxS) extracted from mouse kidney on day 2 post infection"	"source_name_ch1.1"
"Mouse kidneys were homogonized in RNALater solution (Ambion) and bacterial titers were taken.  Samples were pooled, and centrifuged as described below"	"treatment_protocol_ch1.1"