"strain: DY330"	"characteristics_ch1.1"
"tagged gyrase subunit: GyrA-SPA"	"characteristics_ch1.2"
"musgs presence: MuSGS"	"characteristics_ch1.3"
"Raw reads were aligned to the E. coli w3110 MuSGS genome (containing a strong gyrase binding site from bacteriophage Mu) with BWA MEM (default settings)"	"data_processing.1"
"Resulting SAM files were processed with custom script (SAM_to_coverage_and_N5E_N3E.py, github: https://github.com/sutormin94/Gyrase_Topo-seq), giving coverage depth of the genome and N3E values (number of DNA fragments 3'-ends) for every position"	"data_processing.2"
"Gyrase Cleavage Sites (GCSs) were called using custom script (GCSs_calling.py, github: https://github.com/sutormin94/Gyrase_Topo-seq) that takes 4 files (tetrade) as input: +A+IP, +A-IP, -A+IP, -A-IP"	"data_processing.3"
"Genome_build: Escherichia coli W3110 MuSGS (on the basis of NC_007779.1). FASTA and GFF are included on series record."	"data_processing.4"
"Supplementary_files_format_and_content: tar archives contain the following:"	"data_processing.5"
"text wig files contain N3E values (number of DNA fragments 3' ends for each position of the genome)"	"data_processing.6"
"text wig files contain coverage depth data"	"data_processing.7"
"tab-delimited text files with GCSs coordinates, N3E values (\"height of the peak\") and GCSs scores (score of the sequence under the GCS obtained after scanning the genome with DNA-gyrase binding motif)"	"data_processing.8"
"DNA was extracted from resulting supernatant with phenol/chlorophorm method followed by ethanol precipitation. Mock controls (-IP) were made both for +A and for -A: 100 μl aliquots of lysates obtained after sonication were deproteinized and DNA was purified as described earlier. The procedure described gives a quartet of samples (+A+IP, +A-IP, -A+IP, -A-IP), where +A-IP, -A+IP, and -A-IP serves as controls for gyrase poison action and immunoprecipitation."	"extract_protocol_ch1.1"
"Sequencing libraries were prepared with Accel NGS 1S kit (Swift Bioscience) in accordanse with manufacturer’s protocol."	"extract_protocol_ch1.2"
"1 ml of overnight culture was prepared for E. coli DY 330 GyrA-SPA or E. coli DY 330 GyrA-SPA MuSGS by seeding 2YT medium supplemented with antibiotics (kanamycin 50 µg/ml for DY 330 GyrA-SPA and kanamycin 50 µg/ml, chloramphenicol 15 µg/ml for DY 330 GyrA-SPA MuSGS) with cells from one isolate colony."	"growth_protocol_ch1.1"
"Starter was cultivated at 32°C with shaking (180 rpm), then was inoculated into 100 ml of 2YT without antibiotics and cultivation was proceeded under the same conditions until culture reaching mid-logphase (OD600=0.6-0.8)."	"growth_protocol_ch1.2"
"Escherichia coli"	"organism_ch1.1"
"RifCfx_IN_Mu_122mkM_10mkM_3"	"source_name_ch1.1"
"Rifampicine Ciprofloxacin Rep 3 +A-IP"	"title.1"
"When reaching  the optical density indicated (OD600=0.6-0.8) the culture was bisected and DNA gyrase poison (ciprofloxacin, oxolinic acid or microcin B17) was added to the first half (+A samples), while second served as a control (-A samples)."	"treatment_protocol_ch1.1"
"Cultures (+A and -A) were incubated at 32°C with shaking for additional 15 min, then cells were pelleted by centrifugation at 10°C (4500xg) and resuspended in 10 ml of TES buffer (10 mM Tris-Cl pH7.5, 1 mM EDTA, 250 mM NaCl). Washing procedure was repeated twice to remove culture liquid and excess of gyrase poison."	"treatment_protocol_ch1.2"
"Washed pellets were resuspended in 1 ml of TESS buffer (10 mM Tris-Cl pH7.5, 1 mM EDTA, 250 mM NaCl, 0.02% SDS, 0.2% Tween-20) with addition of proteases inhibitors cocktail (cOmplete ultra EDTA free, Roche) and RNAse A (Thermo Scientific). Resulting suspensions were sonicated with parameters optimized to obtain DNA fragments between 200 and 700 bp (SONOPULS HD 3100). Lysates were diluted with 1 ml of TES buffer and 100 μl of ANTI-FLAG® M2 affinity gel (Sigma-Aldrich) was added. Immunoprecipitation was performed for 1.5-2 hours at room temperature with moderate mixing, then affinity gel was washed 4 times by repeating steps of centrifugation (1.5 minute, 1000xg at room temperature) and resuspention (x2 with 1 ml of TESS buffer, x1 with 1 ml of TES buffer, x1 with 1 ml of TE buffer)."	"treatment_protocol_ch1.3"
"Lysates were diluted with 1 ml of TES buffer and 100 μl of ANTI-FLAG® M2 affinity gel (Sigma-Aldrich) was added. Immunoprecipitation was performed for 1.5-2 hours at room temperature with moderate mixing, then affinity gel was washed 4 times by repeating steps of centrifugation (1.5 minute, 1000xg at room temperature) and resuspention (x2 with 1 ml of TESS buffer, x1 with 1 ml of TES buffer, x1 with 1 ml of TE buffer)."	"treatment_protocol_ch1.4"
"For proteolysis, affinity gel obtained after the last centrifugation step was diluted with TES buffer up to final volume 200 μl, proteinase K (Sigma-Aldrich) was added (0.5 mg/ml) and samples were incubated at 55°C for at least 3 hours. After this step samples were centrifuged (2 minutes, 2000xg at room temperature) and supernatants were collected for DNA extraction."	"treatment_protocol_ch1.5"
"ChIP-Seq"	"library_strategy.1"
"strain: DY330"	"characteristics_ch1.1"
"tagged gyrase subunit: GyrA-SPA"	"characteristics_ch1.2"
"musgs presence: MuSGS"	"characteristics_ch1.3"
"1 ml of overnight culture was prepared for E. coli DY 330 GyrA-SPA or E. coli DY 330 GyrA-SPA MuSGS by seeding 2YT medium supplemented with antibiotics (kanamycin 50 µg/ml for DY 330 GyrA-SPA and kanamycin 50 µg/ml, chloramphenicol 15 µg/ml for DY 330 GyrA-SPA MuSGS) with cells from one isolate colony."	"growth_protocol_ch1.1"
"Starter was cultivated at 32°C with shaking (180 rpm), then was inoculated into 100 ml of 2YT without antibiotics and cultivation was proceeded under the same conditions until culture reaching mid-logphase (OD600=0.6-0.8)."	"growth_protocol_ch1.2"
"Escherichia coli"	"organism_ch1.1"
"RifCfx_IN_Mu_122mkM_10mkM_3"	"source_name_ch1.1"
"When reaching  the optical density indicated (OD600=0.6-0.8) the culture was bisected and DNA gyrase poison (ciprofloxacin, oxolinic acid or microcin B17) was added to the first half (+A samples), while second served as a control (-A samples)."	"treatment_protocol_ch1.1"
"Cultures (+A and -A) were incubated at 32°C with shaking for additional 15 min, then cells were pelleted by centrifugation at 10°C (4500xg) and resuspended in 10 ml of TES buffer (10 mM Tris-Cl pH7.5, 1 mM EDTA, 250 mM NaCl). Washing procedure was repeated twice to remove culture liquid and excess of gyrase poison."	"treatment_protocol_ch1.2"
"Washed pellets were resuspended in 1 ml of TESS buffer (10 mM Tris-Cl pH7.5, 1 mM EDTA, 250 mM NaCl, 0.02% SDS, 0.2% Tween-20) with addition of proteases inhibitors cocktail (cOmplete ultra EDTA free, Roche) and RNAse A (Thermo Scientific). Resulting suspensions were sonicated with parameters optimized to obtain DNA fragments between 200 and 700 bp (SONOPULS HD 3100). Lysates were diluted with 1 ml of TES buffer and 100 μl of ANTI-FLAG® M2 affinity gel (Sigma-Aldrich) was added. Immunoprecipitation was performed for 1.5-2 hours at room temperature with moderate mixing, then affinity gel was washed 4 times by repeating steps of centrifugation (1.5 minute, 1000xg at room temperature) and resuspention (x2 with 1 ml of TESS buffer, x1 with 1 ml of TES buffer, x1 with 1 ml of TE buffer)."	"treatment_protocol_ch1.3"
"Lysates were diluted with 1 ml of TES buffer and 100 μl of ANTI-FLAG® M2 affinity gel (Sigma-Aldrich) was added. Immunoprecipitation was performed for 1.5-2 hours at room temperature with moderate mixing, then affinity gel was washed 4 times by repeating steps of centrifugation (1.5 minute, 1000xg at room temperature) and resuspention (x2 with 1 ml of TESS buffer, x1 with 1 ml of TES buffer, x1 with 1 ml of TE buffer)."	"treatment_protocol_ch1.4"
"For proteolysis, affinity gel obtained after the last centrifugation step was diluted with TES buffer up to final volume 200 μl, proteinase K (Sigma-Aldrich) was added (0.5 mg/ml) and samples were incubated at 55°C for at least 3 hours. After this step samples were centrifuged (2 minutes, 2000xg at room temperature) and supernatants were collected for DNA extraction."	"treatment_protocol_ch1.5"