GSE54899-GSM1326335-GPL17439-PMID:25222563.tsv
2.25 KB
"genotype/variation: fur-8myc" "characteristics_ch1.1"
"chip antibody: anti-myc (Santa Cruz Biotech, sc-28207)" "characteristics_ch1.2"
"agent: Fe" "characteristics_ch1.3"
"library strategy: ChIP-exo" "data_processing.1"
"ChIP-exo reads were aligned to the NC_000913 genome reference sequence using using bowtie v1.0.0 with parameters -S" "data_processing.2"
"Genome_build: ASM584v2" "data_processing.3"
"Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.)." "data_processing.4"
"ChIP-seq libraries were prepared for sequencing using standard Illumina protocols" "extract_protocol_ch1.1"
"E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min." "growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655" "organism_ch1.1"
"Immunoprecipitated DNA" "source_name_ch1.1"
"Fur with Fe 1 (ChIP-exo)" "title.1"
"ChIP-Seq" "library_strategy.1"
"genotype/variation: fur-8myc" "characteristics_ch1.1"
"chip antibody: anti-myc (Santa Cruz Biotech, sc-28207)" "characteristics_ch1.2"
"agent: Fe" "characteristics_ch1.3"
"E. coli K-12 MG1655 WT and Fur-8-myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min." "growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655" "organism_ch1.1"
"Immunoprecipitated DNA" "source_name_ch1.1"