GSE84830-GSM2251955-GPL14548-PMID:28911122.tsv
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"growth condition: Exponential + O2" "characteristics_ch1.1"
"treated with: none" "characteristics_ch1.2"
"replicate: 1" "characteristics_ch1.3"
"library strategy: ChIP-exo" "data_processing.1"
"Samples 931, 933, 935 and 937 were aligned with bowtie (V 1.1.2) with parameters --wrapper basic-0 -q -m 1 -l 55 -k 1 -5 3 -3 40 --best -S -p 24, and samples 1311, 1314, 1317 and 1320 were aligned with bowtie (V 1.1.2) with paramters --wrapper basic-0 -q -m 1 -v 2 --best -p 24 -S" "data_processing.2"
"Genome_build: K12 - MG1655" "data_processing.3"
"Supplementary_files_format_and_content: Each wig file contains the alignd reads of each ChIP-exo sample." "data_processing.4"
"The samples were sonicated for a total of 16 minutes and 50 uL protein A/G sepharose. All reactions are performed in an Eppendorf ThermalMixerR while being mixed at 1.4k x rpm. After each reaction, the sepharose was washed with 1 mL of each of the following buffers, leaving 50-100 uL buffer above the sepharose in-between each wash : 1x TE : 10mM Tris-HCl, pH 8.0 + 1 mM EDTA ; 1 x High Salt - 1M NaCl (1% Triton X-100, 50 mM HEPES, pH 8.0, 2 mM EDTA, 0.1% sodium deoxycholate and 1M NaCl) ; 1x Wash Buffer 2 (1% Triton X-100, 50 mM HEPES, pH 8.0, 2 mM EDTA, 0.1% sodium deoxycholate and 0.5M NaCl) ;1x Wash Buffer 3 (1% Triton X-100, 50 mM HEPES, pH 8.0, 2 mM EDTA, 1.0% sodium deoxycholate, 0.25 M LiCl, 1% NP-40, and 10 mM Tris-HCl, pH 8.0) ; 1x TE : 10mM Tris-HCl, pH 8.0 + 1mM EDTA." "extract_protocol_ch1.1"
"The ChIP-exo experiments were generated by following the steps presented by Rhee and Pugh, 2011." "extract_protocol_ch1.2"
"Escherichia coli" "organism_ch1.1"
"Sig70 in E. coli_exponential aerobic growth_no rifampicin" "source_name_ch1.1"
"Sig70 in E. coli, exponential aerobic growth, no rifampicin applied replicate 1 (run 299)" "title.1"
"ChIP-Seq" "library_strategy.1"
"growth condition: Exponential + O2" "characteristics_ch1.1"
"treated with: none" "characteristics_ch1.2"
"replicate: 1" "characteristics_ch1.3"
"Escherichia coli" "organism_ch1.1"
"Sig70 in E. coli_exponential aerobic growth_no rifampicin" "source_name_ch1.1"