"strain: TG-1"	"characteristics_ch1.1"
"strain: TG-2"	"characteristics_ch2.1"
"The average fluorescent signal intensity and local background correction for each spot were obtained using commercially available software from Biodiscovery Inc (Imagene, version 4.0 and Genesight, version 3.5).  Spots with a signal intensity lower than the background signal or those with blemishes were omitted from subsequent analysis.  The mean values from each channel were then log2 transformed and normalised using the LOWESS method to remove intensity-dependent effects in the log2 (ratios) values.  The Cy3/Cy5  (or, for replicates 3 and 4, Cy3/Cy3 ratio) fluorescent ratios were calculated form the normalised values.  Data from independent experiments were combined.  Significance analysis of the data used the Student’s t test to determine the probability that the average of the experimental replicates was significantly different from the average of the control replicates. p-values for the data were calculated by treating each slide as a repeat using Genesight."	"data_processing.1"
"Cells were harvested by centrifugation at 5,000 g for 5 min.  Total RNA was purified using the RNeasy Mini kit (Qiagen) according to the supplier’s protocol (the composition of the RNeasy solutions are unknown).  The supernatant was decanted and 200 μl of TE buffer (10 mM Tris, 1 mM EDTA in DEPC-treated water, pH 8) plus lysosyme (Sigma) was used to resuspend the pellet.  This was mixed vigorously and incubated with intermittent shaking for 5 min at room temperature.  Buffer RLT (700 μl) with β-mercaptoethanol (10 μl of 14.3 M β-mercaptoethanol per 1 ml RTL) was then added to the solution.  The lysate was then mixed with 500 μl of absolute ethanol before applying the solution to an RNeasy Mini column.  This was then centrifuged for 15 s at 8,000 x g.  Buffer RW1 (700 μl) was applied to the column and centrifuged to wash the RNA.  At this point an RNase-free DNase on-column digest (Qiagen) was carried out, before the wash process was repeated twice with 500 μl of RPE buffer.  The RNA was eluted twice in one 30 μl volume of RNase-free water and stored at -70 oC."	"extract_protocol_ch1.1"
"Cells were harvested by centrifugation at 5,000 g for 5 min.  Total RNA was purified using the RNeasy Mini kit (Qiagen) according to the supplier’s protocol (the composition of the RNeasy solutions are unknown).  The supernatant was decanted and 200 μl of TE buffer (10 mM Tris, 1 mM EDTA in DEPC-treated water, pH 8) plus lysosyme (Sigma) was used to resuspend the pellet.  This was mixed vigorously and incubated with intermittent shaking for 5 min at room temperature.  Buffer RLT (700 μl) with β-mercaptoethanol (10 μl of 14.3 M β-mercaptoethanol per 1 ml RTL) was then added to the solution.  The lysate was then mixed with 500 μl of absolute ethanol before applying the solution to an RNeasy Mini column.  This was then centrifuged for 15 s at 8,000 x g.  Buffer RW1 (700 μl) was applied to the column and centrifuged to wash the RNA.  At this point an RNase-free DNase on-column digest (Qiagen) was carried out, before the wash process was repeated twice with 500 μl of RPE buffer.  The RNA was eluted twice in one 30 μl volume of RNase-free water and stored at -70 oC."	"extract_protocol_ch2.1"
"Biofilms were grown on nylon membranes using agar as the source of nutrients and water.  Aliquots of 10 ml Luria agar were transferred to petri dishes to produce layers of agar approximately 3 mm in depth.  Nylon membrane filters (47 mm diameter) with a 0.2 μm pore size (Whatman) were autoclaved in Milli-Q water, dried and placed on the agar surface.  A 100 μl aliquot of an overnight culture (approximately 108 cells) was applied to the membrane as a single spot and allowed to dry.  All of these steps were performed on a level table so as not to introduce unwanted gradients.  Dishes were then inverted and incubated at 37 oC for 24 h."	"growth_protocol_ch1.1"
"Biofilms were grown on nylon membranes using agar as the source of nutrients and water.  Aliquots of 10 ml Luria agar were transferred to petri dishes to produce layers of agar approximately 3 mm in depth.  Nylon membrane filters (47 mm diameter) with a 0.2 μm pore size (Whatman) were autoclaved in Milli-Q water, dried and placed on the agar surface.  A 100 μl aliquot of an overnight culture (approximately 108 cells) was applied to the membrane as a single spot and allowed to dry.  All of these steps were performed on a level table so as not to introduce unwanted gradients.  Dishes were then inverted and incubated at 37 oC for 24 h."	"growth_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"Escherichia coli Colony Biofilm Interior"	"source_name_ch1.1"
"Escherichia coli Colony Biofilm Perimeter"	"source_name_ch2.1"
"Colony Biofilm Replicate 4"	"title.1"
"Biofilms were individually removed from the incubator and, using a small scalpel blade and sterile forceps, the distinctive outer perimeter of biofilm growth was cut away from the rest of the biofilm.  The two resulting sections of membrane were submerged in separate volumes of RNAprotect Bacteria Reagent and vortexed to release the cells.  The sections of membrane were then removed from the resulting suspension before RNA extraction."	"treatment_protocol_ch1.1"
"Biofilms were individually removed from the incubator and, using a small scalpel blade and sterile forceps, the distinctive outer perimeter of biofilm growth was cut away from the rest of the biofilm.  The two resulting sections of membrane were submerged in separate volumes of RNAprotect Bacteria Reagent and vortexed to release the cells.  The sections of membrane were then removed from the resulting suspension before RNA extraction."	"treatment_protocol_ch2.1"
"strain: TG-1"	"characteristics_ch1.1"
"strain: TG-2"	"characteristics_ch2.1"
"Biofilms were grown on nylon membranes using agar as the source of nutrients and water.  Aliquots of 10 ml Luria agar were transferred to petri dishes to produce layers of agar approximately 3 mm in depth.  Nylon membrane filters (47 mm diameter) with a 0.2 μm pore size (Whatman) were autoclaved in Milli-Q water, dried and placed on the agar surface.  A 100 μl aliquot of an overnight culture (approximately 108 cells) was applied to the membrane as a single spot and allowed to dry.  All of these steps were performed on a level table so as not to introduce unwanted gradients.  Dishes were then inverted and incubated at 37 oC for 24 h."	"growth_protocol_ch1.1"
"Biofilms were grown on nylon membranes using agar as the source of nutrients and water.  Aliquots of 10 ml Luria agar were transferred to petri dishes to produce layers of agar approximately 3 mm in depth.  Nylon membrane filters (47 mm diameter) with a 0.2 μm pore size (Whatman) were autoclaved in Milli-Q water, dried and placed on the agar surface.  A 100 μl aliquot of an overnight culture (approximately 108 cells) was applied to the membrane as a single spot and allowed to dry.  All of these steps were performed on a level table so as not to introduce unwanted gradients.  Dishes were then inverted and incubated at 37 oC for 24 h."	"growth_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"Escherichia coli Colony Biofilm Interior"	"source_name_ch1.1"
"Escherichia coli Colony Biofilm Perimeter"	"source_name_ch2.1"
"Biofilms were individually removed from the incubator and, using a small scalpel blade and sterile forceps, the distinctive outer perimeter of biofilm growth was cut away from the rest of the biofilm.  The two resulting sections of membrane were submerged in separate volumes of RNAprotect Bacteria Reagent and vortexed to release the cells.  The sections of membrane were then removed from the resulting suspension before RNA extraction."	"treatment_protocol_ch1.1"
"Biofilms were individually removed from the incubator and, using a small scalpel blade and sterile forceps, the distinctive outer perimeter of biofilm growth was cut away from the rest of the biofilm.  The two resulting sections of membrane were submerged in separate volumes of RNAprotect Bacteria Reagent and vortexed to release the cells.  The sections of membrane were then removed from the resulting suspension before RNA extraction."	"treatment_protocol_ch2.1"