"test: ChIP DNA"	"characteristics_ch1.1"
"condition: nitrogen-limiting condition without rifampicin treatment"	"characteristics_ch1.2"
"strain: MG1655"	"characteristics_ch1.3"
"antibody: RNAP beta subunit (NT63)"	"characteristics_ch1.4"
"reference: Input DNA"	"characteristics_ch2.1"
"condition: nitrogen-limiting condition without rifampicin treatment"	"characteristics_ch2.2"
"strain: MG1655"	"characteristics_ch2.3"
"antibody: IgG"	"characteristics_ch2.4"
"The raw data (.pair file) was subjected to per channel quantile normalization (Bolstad et al. Bioinformatics 19(2):185), IP/mock-IP ratio computation and enriched region identification as implemented in the NimbleScan software package, version 2.4.27 (www.nimblegen.com)."	"data_processing.1"
"Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min. The cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug/mL RNaseA, protease inhibitor cocktail (Sigma) and 1 kU Ready-LyseTM lysozyme (Epicentre). The cells were incubated at room temperature for 30 min and then treated with 0.5 mL of 2XIP buffer with the protease inhibitor cocktail. The lysate was then sonicated four times for 20 sec each in an ice bath to fragment the chromatin complexes using Misonix sonicator 3000 (output level = 2.5). The range of the DNA size resulting from the sonication procedure was 300 – 1000 bp. 6 uL of mouse antibody (NT63, Neoclone) was used to immunoprecipitate the chromatin complex of RNA polymerase subunit (rpoB) and DNA. For the control (mock-IP), 2 ug of normal mouse IgG (Upstate) was added into the cell extract. IP DNAs were purified with QIAquick PCR Purification Kit (Qiagen) then amplified PCR."	"extract_protocol_ch1.1"
"Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min. The cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug/mL RNaseA, protease inhibitor cocktail (Sigma) and 1 kU Ready-LyseTM lysozyme (Epicentre). The cells were incubated at room temperature for 30 min and then treated with 0.5 mL of 2XIP buffer with the protease inhibitor cocktail. The lysate was then sonicated four times for 20 sec each in an ice bath to fragment the chromatin complexes using Misonix sonicator 3000 (output level = 2.5). The range of the DNA size resulting from the sonication procedure was 300 – 1000 bp. 6 uL of mouse antibody (NT63, Neoclone) was used to immunoprecipitate the chromatin complex of RNA polymerase subunit (rpoB) and DNA. For the control (mock-IP), 2 ug of normal mouse IgG (Upstate) was added into the cell extract. IP DNAs were purified with QIAquick PCR Purification Kit (Qiagen) then amplified PCR."	"extract_protocol_ch2.1"
"E. coli MG1655 strain was cultured in W2 minimal medium (for nitrogen-limiting condition) at 37 °C with constant agitation and harvested at mid-exponential phase. (OD600nm ~ 0.6) (Powell, B. S. et al. J of Biol. Chem.270(9):4822)"	"growth_protocol_ch1.1"
"E. coli MG1655 strain was cultured in W2 minimal medium (for nitrogen-limiting condition) at 37 °C with constant agitation and harvested at mid-exponential phase. (OD600nm ~ 0.6) (Powell, B. S. et al. J of Biol. Chem.270(9):4822)"	"growth_protocol_ch2.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch2.1"
"E.coli RNAP beta subunit ChIP DNA from nitrogen-limiting condition without rifampicin treatment"	"source_name_ch1.1"
"Input DNA from nitrogen-limiting condition without rifampicin treatment"	"source_name_ch2.1"
"E.coli_nitrogen_dynamic_1"	"title.1"
"Cross-linked and sonicated chromatin complex of RNAP beta-subunit and DNA was immunoprecipitated by NT63 mouse antibody."	"treatment_protocol_ch1.1"
"Cross-linked and sonicated chromatin complex of RNAP beta-subunit and DNA was immunoprecipitated by normal mouse IgG (Upstate) for the control (mock-IP)."	"treatment_protocol_ch2.1"
"test: ChIP DNA"	"characteristics_ch1.1"
"condition: nitrogen-limiting condition without rifampicin treatment"	"characteristics_ch1.2"
"strain: MG1655"	"characteristics_ch1.3"
"antibody: RNAP beta subunit (NT63)"	"characteristics_ch1.4"
"reference: Input DNA"	"characteristics_ch2.1"
"condition: nitrogen-limiting condition without rifampicin treatment"	"characteristics_ch2.2"
"strain: MG1655"	"characteristics_ch2.3"
"antibody: IgG"	"characteristics_ch2.4"
"E. coli MG1655 strain was cultured in W2 minimal medium (for nitrogen-limiting condition) at 37 °C with constant agitation and harvested at mid-exponential phase. (OD600nm ~ 0.6) (Powell, B. S. et al. J of Biol. Chem.270(9):4822)"	"growth_protocol_ch1.1"
"E. coli MG1655 strain was cultured in W2 minimal medium (for nitrogen-limiting condition) at 37 °C with constant agitation and harvested at mid-exponential phase. (OD600nm ~ 0.6) (Powell, B. S. et al. J of Biol. Chem.270(9):4822)"	"growth_protocol_ch2.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch2.1"
"E.coli RNAP beta subunit ChIP DNA from nitrogen-limiting condition without rifampicin treatment"	"source_name_ch1.1"
"Input DNA from nitrogen-limiting condition without rifampicin treatment"	"source_name_ch2.1"
"Cross-linked and sonicated chromatin complex of RNAP beta-subunit and DNA was immunoprecipitated by NT63 mouse antibody."	"treatment_protocol_ch1.1"
"Cross-linked and sonicated chromatin complex of RNAP beta-subunit and DNA was immunoprecipitated by normal mouse IgG (Upstate) for the control (mock-IP)."	"treatment_protocol_ch2.1"