"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: static petri dish (disposable)"	"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: static petri dish (disposable)"	"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 inoculation and were inoculated into 5 ml 10% LB in a disposable petri dish (60 mm x 15 mm). 50 ul E. coli culture was inoculated for mono-species pure culture. 50 ul E. coli and 10 ul S. maltophilia were mixed and inoculated for mixed-species culture. Petri dishes were set static at room temperature (20 C) for 18 h for biofilm growth."	"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 inoculation and were inoculated into 5 ml 10% LB in a disposable petri dish (60 mm x 15 mm). 50 ul E. coli culture was inoculated for mono-species pure culture. 50 ul E. coli and 10 ul S. maltophilia were mixed and inoculated for mixed-species culture. Petri dishes were set static at room temperature (20 C) for 18 h for biofilm growth."	"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 biofilms 1"	"source_name_ch1.1"
"sorted E. coli cells from dual-species biofilms 1"	"source_name_ch2.1"
"Escherichia coli_MixedSpeciesBiofilm_bioreplicate1_techreplicate_2"	"title.1"
"Suspended cells were then removed and biofilms were washed 3 times with 1 ml 10% LB broth. Biofilms from each petri dish were then scraped into a vial containing 1 ml 10% LB. Scraped biofilms in each vial were concentrated from 1 ml into 50 ul by centrifugation. 500 ul RNAlater was added and mixed well. Samples in RNAlater were kept in 4C fridge overnight.  Each vial was homogenized with OMNI TH homogenizer for 2 min on ice and further aliquoted into small vials. 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 extractions."	"treatment_protocol_ch1.1"
"Suspended cells were then removed and biofilms were washed 3 times with 1 ml 10% LB broth. Biofilms from each petri dish were then scraped into a vial containing 1 ml 10% LB. Scraped biofilms in each vial were concentrated from 1 ml into 50 ul by centrifugation. 500 ul RNAlater was added and mixed well. Samples in RNAlater were kept in 4C fridge overnight.  Each vial was homogenized with OMNI TH homogenizer for 2 min on ice and further aliquoted into small vials. 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 extractions."	"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: static petri dish (disposable)"	"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: static petri dish (disposable)"	"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 inoculation and were inoculated into 5 ml 10% LB in a disposable petri dish (60 mm x 15 mm). 50 ul E. coli culture was inoculated for mono-species pure culture. 50 ul E. coli and 10 ul S. maltophilia were mixed and inoculated for mixed-species culture. Petri dishes were set static at room temperature (20 C) for 18 h for biofilm growth."	"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 inoculation and were inoculated into 5 ml 10% LB in a disposable petri dish (60 mm x 15 mm). 50 ul E. coli culture was inoculated for mono-species pure culture. 50 ul E. coli and 10 ul S. maltophilia were mixed and inoculated for mixed-species culture. Petri dishes were set static at room temperature (20 C) for 18 h for biofilm growth."	"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 biofilms 1"	"source_name_ch1.1"
"sorted E. coli cells from dual-species biofilms 1"	"source_name_ch2.1"
"Suspended cells were then removed and biofilms were washed 3 times with 1 ml 10% LB broth. Biofilms from each petri dish were then scraped into a vial containing 1 ml 10% LB. Scraped biofilms in each vial were concentrated from 1 ml into 50 ul by centrifugation. 500 ul RNAlater was added and mixed well. Samples in RNAlater were kept in 4C fridge overnight.  Each vial was homogenized with OMNI TH homogenizer for 2 min on ice and further aliquoted into small vials. 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 extractions."	"treatment_protocol_ch1.1"
"Suspended cells were then removed and biofilms were washed 3 times with 1 ml 10% LB broth. Biofilms from each petri dish were then scraped into a vial containing 1 ml 10% LB. Scraped biofilms in each vial were concentrated from 1 ml into 50 ul by centrifugation. 500 ul RNAlater was added and mixed well. Samples in RNAlater were kept in 4C fridge overnight.  Each vial was homogenized with OMNI TH homogenizer for 2 min on ice and further aliquoted into small vials. 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 extractions."	"treatment_protocol_ch2.1"