"strain: K-12 PHL644/pMP4655"	"characteristics_ch1.1"
"growth mode: planktonic culture in annular reactor"	"characteristics_ch1.2"
"growth time: 7-day"	"characteristics_ch1.3"
"treatment: sorted"	"characteristics_ch1.4"
"strain: K-12 PHL644/pMP4655"	"characteristics_ch2.1"
"growth mode: planktonic culture in annular reactor"	"characteristics_ch2.2"
"growth time: 7-day"	"characteristics_ch2.3"
"treatment: non-sorted"	"characteristics_ch2.4"
"Data was analyzed in the software Acuity 4.0 (Molecular Devices, Sunnyvale, CA). LOWESS normalization was performed with three iterations using a smoothing factor of 0.4. Hybridized spots having a high QC (quality control) value >0.1, good flag tags (A, B and C) in both Cy3/Cy5 channels were chosen for further analysis. One sample t-tests were performed across replicates. Step-down Bonferroni-Holm was used for the correction of multiple hypotheses testing. Only oligonucleotides for E. coli K12 were choosen to draw conclusion."	"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"
"E. coli cells were grown in annular reactor (BioSurface Technologies, Bozeman, MT) inoculated with 1 ml overnight cultures and supplied with fresh 10-fold diluted Luria broth at 100 ml/h at room temperature for 7-days. Cells were harvested onto membrane filters (pore size 0.45 micrometer) after pre-filtering out aggregates larger than 5 micrometer from planktonic cultures in the reactor. Cells were re-suspended in RNAlater after harvest and stored at 4 degree C overnight."	"growth_protocol_ch1.1"
"E. coli cells were grown in annular reactor (BioSurface Technologies, Bozeman, MT) inoculated with 1 ml overnight cultures and supplied with fresh 10-fold diluted Luria broth at 100 ml/h at room temperature for 7-days. Cells were harvested onto membrane filters (pore size 0.45 micrometer) after pre-filtering out aggregates larger than 5 micrometer from planktonic cultures in the reactor. Cells were re-suspended in RNAlater after harvest and stored at 4 degree C overnight."	"growth_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"sorted E. coli cells from culture 2"	"source_name_ch1.1"
"non-sorted E. coli cells from culture 2"	"source_name_ch2.1"
"sorted vs. non-sorted cells bioreplicate 2 technical replicate 2"	"title.1"
"Cells in RNAlater were aliquoted into two. One served as non-sorted cells and kept at 4 degree C. The other aliquot 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 and microbeads, followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater."	"treatment_protocol_ch1.1"
"Cells in RNAlater were aliquoted into two. One served as non-sorted cells and kept at 4 degree C. The other aliquot 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 and microbeads, followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater."	"treatment_protocol_ch2.1"
"strain: K-12 PHL644/pMP4655"	"characteristics_ch1.1"
"growth mode: planktonic culture in annular reactor"	"characteristics_ch1.2"
"growth time: 7-day"	"characteristics_ch1.3"
"treatment: sorted"	"characteristics_ch1.4"
"strain: K-12 PHL644/pMP4655"	"characteristics_ch2.1"
"growth mode: planktonic culture in annular reactor"	"characteristics_ch2.2"
"growth time: 7-day"	"characteristics_ch2.3"
"treatment: non-sorted"	"characteristics_ch2.4"
"E. coli cells were grown in annular reactor (BioSurface Technologies, Bozeman, MT) inoculated with 1 ml overnight cultures and supplied with fresh 10-fold diluted Luria broth at 100 ml/h at room temperature for 7-days. Cells were harvested onto membrane filters (pore size 0.45 micrometer) after pre-filtering out aggregates larger than 5 micrometer from planktonic cultures in the reactor. Cells were re-suspended in RNAlater after harvest and stored at 4 degree C overnight."	"growth_protocol_ch1.1"
"E. coli cells were grown in annular reactor (BioSurface Technologies, Bozeman, MT) inoculated with 1 ml overnight cultures and supplied with fresh 10-fold diluted Luria broth at 100 ml/h at room temperature for 7-days. Cells were harvested onto membrane filters (pore size 0.45 micrometer) after pre-filtering out aggregates larger than 5 micrometer from planktonic cultures in the reactor. Cells were re-suspended in RNAlater after harvest and stored at 4 degree C overnight."	"growth_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"sorted E. coli cells from culture 2"	"source_name_ch1.1"
"non-sorted E. coli cells from culture 2"	"source_name_ch2.1"
"Cells in RNAlater were aliquoted into two. One served as non-sorted cells and kept at 4 degree C. The other aliquot 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 and microbeads, followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater."	"treatment_protocol_ch1.1"
"Cells in RNAlater were aliquoted into two. One served as non-sorted cells and kept at 4 degree C. The other aliquot 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 and microbeads, followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater."	"treatment_protocol_ch2.1"