|
| Status |
Public on Dec 20, 2019 |
| Title |
IHMA_Erf_I_3 |
| Sample type |
SRA |
| |
|
| Source name |
purified genomic DNA from liquid cultures
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: IHMA879472
erfa origin: P. aeruginosa
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Purified proteins bound to magnetic beads were 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
I_E_I_processed.xlsx
|
| Data processing |
Library strategy: DAP-seq
Read trimming using Trimmomatic
Alignment using Bowtie2
Peak calling using MACS2
closest features called with BEDtools
Genome_build: IHMA879472, PAO1b, PA23, CHA0, KT2440
Supplementary_files_format_and_content: excel table, MACS2 analysis results with closest features
|
| |
|
| Submission date |
Sep 18, 2019 |
| Last update date |
Dec 20, 2019 |
| 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) |
| GSE137648 |
Determination of ErfA regulon by DAP-seq in several Pseudomonas species |
|
| Relations |
| BioSample |
SAMN12781123 |
| SRA |
SRX6865332 |
