"culture time: 18 h"	"characteristics_ch1.1"
"culture temperature: room temperature (20 C)"	"characteristics_ch1.2"
"culture media: 10% Luria broth"	"characteristics_ch1.3"
"culture system: flask with continuous shaking (250 rpm)"	"characteristics_ch1.4"
"treatment: with homogenization and separation"	"characteristics_ch1.5"
"culture time: 18 h"	"characteristics_ch2.1"
"culture temperature: room temperature (20 C)"	"characteristics_ch2.2"
"culture media: 10% Luria broth"	"characteristics_ch2.3"
"culture system: flask with continous shaking (250 rpm)"	"characteristics_ch2.4"
"treatment: with homogenization and separation"	"characteristics_ch2.5"
"Data was analyzed in the software Acuity 4.0 (Molecular Devices, Sunnyvale, CA). Hybridized spots for E. coli K12 having a high QC (quality control) value >0.1, good flag tags (A, B and C) in both Cy3/Cy5 channels were chosen for analysis. LOWESS normalization was performed with three iterations using a smoothing factor of 0.4.  One sample t-tests were performed across replicates. P-value of 0.05 was chosen as the significant level."	"data_processing.1"
"RNAlater was removed from cells by filtration. Total RNA was extracted from cells using a hot SDS/phenol protocol (http://www.genome.wisc.edu/pub/reprints/) with an additional 1-min bead-beating. Chemical extractions were performed in phase lock gels (Fisher Scientific, Pittsburgh, PA)."	"extract_protocol_ch1.1"
"RNAlater was removed from cells by filtration. Total RNA was extracted from cells using a hot SDS/phenol protocol (http://www.genome.wisc.edu/pub/reprints/) with an additional 1-min bead-beating. Chemical extractions were performed in phase lock gels (Fisher Scientific, Pittsburgh, PA)."	"extract_protocol_ch2.1"
"Cells for inoculation were from overnight planktonic culture in 10% Luria-Bertani broth at 30 degree Celsius. Cells were washed in equal volume of fresh 10% LB broth before inoculated into 30 ml 10% LB in a flask. 300 ul E. coli culture was inoculated for mono-species pure culture. 150 ul E. coli and 60 ul S. maltophilia were mixed and inoculated for mixed-species cultures. Flasks were set on a shaker (250 rpm) at room temperature (20 C) for 18 h."	"growth_protocol_ch1.1"
"Cells for inoculation were from overnight planktonic culture in 10% Luria-Bertani broth at 30 degree Celsius. Cells were washed in equal volume of fresh 10% LB broth before inoculated into 30 ml 10% LB in a flask. 300 ul E. coli culture was inoculated for mono-species pure culture. 150 ul E. coli and 60 ul S. maltophilia were mixed and inoculated for mixed-species cultures. Flasks were set on a shaker (250 rpm) at room temperature (20 C) for 18 h."	"growth_protocol_ch2.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Escherichia coli K-12"	"organism_ch2.1"
"sorted E. coli cells from mono-species pure planktonic culture 1"	"source_name_ch1.1"
"sorted E. coli cells from dual-species planktonic culture 1"	"source_name_ch2.1"
"Escherichia coli_MixedSpeciesPlanktonic_bioreplicate1_techreplicate_1"	"title.1"
"Cells were harvested and resuspended in RNAlater and kept in 4C fridge overnight. Cells were aliquoted into vials containing around 2x10^8 cells. Cells in each vial were then re-suspended in nuclease-free phosphate buffered saline, incubated with anti-E. coli antibody (ViroStat) and microbeads (Miltenyi), followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater until RNA extraction."	"treatment_protocol_ch1.1"
"Cells were harvested and resuspended in RNAlater and kept in 4C fridge overnight. Cells were aliquoted into vials containing around 2x10^8 cells. Cells in each vial were then re-suspended in nuclease-free phosphate buffered saline, incubated with anti-E. coli antibody (ViroStat) and microbeads (Miltenyi), followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater until RNA extraction."	"treatment_protocol_ch2.1"
"culture time: 18 h"	"characteristics_ch1.1"
"culture temperature: room temperature (20 C)"	"characteristics_ch1.2"
"culture media: 10% Luria broth"	"characteristics_ch1.3"
"culture system: flask with continuous shaking (250 rpm)"	"characteristics_ch1.4"
"treatment: with homogenization and separation"	"characteristics_ch1.5"
"culture time: 18 h"	"characteristics_ch2.1"
"culture temperature: room temperature (20 C)"	"characteristics_ch2.2"
"culture media: 10% Luria broth"	"characteristics_ch2.3"
"culture system: flask with continous shaking (250 rpm)"	"characteristics_ch2.4"
"treatment: with homogenization and separation"	"characteristics_ch2.5"
"Cells for inoculation were from overnight planktonic culture in 10% Luria-Bertani broth at 30 degree Celsius. Cells were washed in equal volume of fresh 10% LB broth before inoculated into 30 ml 10% LB in a flask. 300 ul E. coli culture was inoculated for mono-species pure culture. 150 ul E. coli and 60 ul S. maltophilia were mixed and inoculated for mixed-species cultures. Flasks were set on a shaker (250 rpm) at room temperature (20 C) for 18 h."	"growth_protocol_ch1.1"
"Cells for inoculation were from overnight planktonic culture in 10% Luria-Bertani broth at 30 degree Celsius. Cells were washed in equal volume of fresh 10% LB broth before inoculated into 30 ml 10% LB in a flask. 300 ul E. coli culture was inoculated for mono-species pure culture. 150 ul E. coli and 60 ul S. maltophilia were mixed and inoculated for mixed-species cultures. Flasks were set on a shaker (250 rpm) at room temperature (20 C) for 18 h."	"growth_protocol_ch2.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Escherichia coli K-12"	"organism_ch2.1"
"sorted E. coli cells from mono-species pure planktonic culture 1"	"source_name_ch1.1"
"sorted E. coli cells from dual-species planktonic culture 1"	"source_name_ch2.1"
"Cells were harvested and resuspended in RNAlater and kept in 4C fridge overnight. Cells were aliquoted into vials containing around 2x10^8 cells. Cells in each vial were then re-suspended in nuclease-free phosphate buffered saline, incubated with anti-E. coli antibody (ViroStat) and microbeads (Miltenyi), followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater until RNA extraction."	"treatment_protocol_ch1.1"
"Cells were harvested and resuspended in RNAlater and kept in 4C fridge overnight. Cells were aliquoted into vials containing around 2x10^8 cells. Cells in each vial were then re-suspended in nuclease-free phosphate buffered saline, incubated with anti-E. coli antibody (ViroStat) and microbeads (Miltenyi), followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater until RNA extraction."	"treatment_protocol_ch2.1"