|
| Status |
Public on Jan 05, 2023 |
| Title |
RpoD cytosine 2 (ChIP-exo) |
| Sample type |
SRA |
| |
|
| Source name |
Immunoprecipitated DNA
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
nitrogen source: cytosine
genotype/variation: WT
chip antibody: anti-RpoD (Neoclone, WP004)
|
| Growth protocol |
E. coli K-12 MG1655 WT, NtrC-8myc and Nac-8myc tagged strains were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media with 0.2% glucose and 2 g/L glutamine, cytidine or cytosine, or ammonia for nitrogen source.
|
| 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 |
| |
|
| Description |
processed data file: chipexo_rpod_binding.csv
|
| Data processing |
library strategy: ChIP-exo
ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters -S
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity for NtrC, Nac, RpoN and 90% strongest intensity for RpoD were used as background intensity.
For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build: ASM584v2
Supplementary_files_format_and_content: Comma-delimited text files (peaks) include binding positions and intensity values for each sample.
|
| |
|
| Submission date |
Feb 12, 2014 |
| Last update date |
Jan 05, 2023 |
| 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) |
| GSE54902 |
Elucidating transcriptional regulation of nitrogen metabolism with systems approaches [ChIP-Seq] |
| GSE54905 |
Elucidating transcriptional regulation of nitrogen metabolism with systems approaches |
|
| Relations |
| BioSample |
SAMN02640308 |
| SRA |
SRX469877 |
