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Series GSE117186 Query DataSets for GSE117186
Status Public on Jul 17, 2018
Title Topo-Seq application for topoisomerases binding sites identification with a single-nucleotide resolution
Organism Escherichia coli
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Topo-Seq is a ChIP-Seq-based methodology that allows high-throughput identification of topoisomerases binding (cleavage) sites with a single-base precision. On a first stage of the project DNA-gyrase binding sites on a Escherichia coli DY330 genome are investigated.
Overall design Escherichia coli DY330 cultures were treated with a range of DNA-gyrase poisons (ciprofloxacin, microcin B17, oxolinic acid) during exponential phase (OD600=0.6), than cells were harvested and lysed with sonication. Complexes of gyrase with DNA were immunoprecipitated using ANTI-FLAG M2 affinnity resin, proteins were degraded with proteinase K and DNA extracted by phenol-chlorophorm followed by precipitation in alcohol. Lybraries from the DNA recovered were prepared using NGS Accel 1S Plus DNA kit (Swift Bioscience). Reads were mapped to E. coli w3110 MuSGS genome (with BWA MEM), signals (Gyrase Cleavage Sites - GCSs) were identified using Audic-Claveiry statistic (custom scripts with detailed descriptions could be found at
Contributor(s) Sutormin D, Ghilarov D
Citation(s) 30517674
Submission date Jul 16, 2018
Last update date Apr 24, 2019
Contact name Dmitry Sutormin
Phone +79154072592
Organization name Skolkovo Institute of Science and Technology
Department Life Sciences
Street address Nobelya Ulitsa 3
City Moscow
ZIP/Postal code 121205
Country Russia
Platforms (1)
GPL21222 Illumina NextSeq 500 (Escherichia coli)
Samples (31)
GSM3273132 Untreated Rep 1 -A+IP
GSM3273133 Untreated Rep 1 -A-IP
GSM3273134 Untreated Rep 2 -A+IP
BioProject PRJNA481368
SRA SRP153994

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE117186_E_coli_w3110_G_Mu.fasta.gz 1.4 Mb (ftp)(http) FASTA
GSE117186_Escherichia_coli_K_12_w3110_Mu_genes_annotation.gff.gz 345.2 Kb (ftp)(http) GFF
GSE117186_RAW.tar 145.5 Mb (http)(custom) TAR (of TAR)
GSE117186_supplementary_Sample_sets_description.xlsx 12.6 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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