|
| Status |
Public on Sep 09, 2014 |
| Title |
RpoB with DPD 1 (ChIP-exo) |
| Sample type |
SRA |
| |
|
| Source name |
Immunoprecipitated DNA
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
genotype/variation: WT
chip antibody: anti-RpoB (Neoclone, WP002)
agent: DPD
|
| Growth protocol |
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.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
library strategy: ChIP-exo
ChIP-exo reads were aligned to the NC_000913 genome reference sequence using using bowtie v1.0.0 with parameters -S
Genome_build: ASM584v2
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(.).
|
| |
|
| Submission date |
Feb 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Donghyuk Kim |
| E-mail(s) |
[email protected]
|
| Organization name |
UNIST
|
| Department |
Department of Chemical Engineering
|
| Lab |
Systems Biology Lab
|
| Street address |
50 UNIST-gil, Eonyang-eup, Ulju-gun
|
| City |
Ulsan |
| ZIP/Postal code |
44919 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17439 |
| Series (2) |
| GSE54899 |
Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [ChIP-Seq] |
| GSE54901 |
Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli |
|
| Relations |
| BioSample |
SAMN02640291 |
| SRA |
SRX469834 |
