"genotype: Lrp-8myc"	"characteristics_ch1.1"
"antibody: 9E10 Myc tag antibody"	"characteristics_ch1.2"
"treatment: glucose (2 g/L) minimal M9 medium supplemented without 10 mM leucine."	"characteristics_ch1.3"
"genotype: Lrp-8myc"	"characteristics_ch2.1"
"antibody: normal mouse IgG"	"characteristics_ch2.2"
"antibody manufacturer: Upstate"	"characteristics_ch2.3"
"treatment: glucose (2 g/L) minimal M9 medium supplemented without 10 mM leucine."	"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 strains harboring Lrp-8myc were grown in glucose (2 g/L) minimal M9 medium supplemented without 10 mM leucine."	"growth_protocol_ch1.1"
"E. coli strains harboring Lrp-8myc were grown in glucose (2 g/L) minimal M9 medium supplemented without 10 mM leucine."	"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 Lrp ChIP DNA NH4Cl 3"	"source_name_ch1.1"
"E. Coli Lrp ChIP DNA NH4Cl 3"	"source_name_ch2.1"
"Lrp_NH4Cl_3"	"title.1"
"Cross-linked and sonicated chromatin complex of Lrp-8myc and DNA was immunoprecipitated by 9E10 myc antibody."	"treatment_protocol_ch1.1"
"Cross-linked and sonicated chromatin complex of Lrp-8myc and DNA was immunoprecipitated by using normal mouse IgG for the control."	"treatment_protocol_ch2.1"
"genotype: Lrp-8myc"	"characteristics_ch1.1"
"antibody: 9E10 Myc tag antibody"	"characteristics_ch1.2"
"treatment: glucose (2 g/L) minimal M9 medium supplemented without 10 mM leucine."	"characteristics_ch1.3"
"genotype: Lrp-8myc"	"characteristics_ch2.1"
"antibody: normal mouse IgG"	"characteristics_ch2.2"
"antibody manufacturer: Upstate"	"characteristics_ch2.3"
"treatment: glucose (2 g/L) minimal M9 medium supplemented without 10 mM leucine."	"characteristics_ch2.4"
"E. coli strains harboring Lrp-8myc were grown in glucose (2 g/L) minimal M9 medium supplemented without 10 mM leucine."	"growth_protocol_ch1.1"
"E. coli strains harboring Lrp-8myc were grown in glucose (2 g/L) minimal M9 medium supplemented without 10 mM leucine."	"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 Lrp ChIP DNA NH4Cl 3"	"source_name_ch1.1"
"E. Coli Lrp ChIP DNA NH4Cl 3"	"source_name_ch2.1"
"Cross-linked and sonicated chromatin complex of Lrp-8myc and DNA was immunoprecipitated by 9E10 myc antibody."	"treatment_protocol_ch1.1"
"Cross-linked and sonicated chromatin complex of Lrp-8myc and DNA was immunoprecipitated by using normal mouse IgG for the control."	"treatment_protocol_ch2.1"