|
| Status |
Public on Jul 27, 2021 |
| Title |
CS41_PmrA-IHMA87_05256_IHMA87_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
purified genomic DNA from liquid cultures
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: IHMA87
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After cell-fre protein expression, soluble His-tagged proteins were bound to cobalt magnetic beads and incubated with adaptor-ligated sheared genomic DNA. After washes and isolation of bead-protein-DNA complexes, the bound DNA regions were eluted by heating and then used for library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
adaptor-ligated sheared genomic DNA
|
| Data processing |
Library strategy: DAP-seq
Read trimming using Trimmomatic
Alignment using Bowtie2
Peak calling using MACS2
closest features called with BEDtools
Genome_build: PAO1, PA14, IHMA87
Supplementary_files_format_and_content: excel table, list of RRs binding to the promoter region of each gene
|
| |
|
| Submission date |
Jun 27, 2021 |
| Last update date |
Jul 27, 2021 |
| Contact name |
Julian Trouillon |
| Organization name |
ETH Zurich
|
| Department |
Institute of Molecular Systems Biology
|
| Street address |
Otto-Stern-Weg 3
|
| City |
Zurich |
| ZIP/Postal code |
8093 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21297 |
| Series (1) |
| GSE179001 |
Determination of the regulons of 55 response regulators from P. aeruginosa by DAP-seq |
|
| Relations |
| BioSample |
SAMN19906729 |
| SRA |
SRX11239039 |
