|
| Status |
Public on Oct 01, 2020 |
| Title |
Psest_4132_3 |
| Sample type |
SRA |
| |
|
| Source name |
purified genomic DNA from liquid cultures
|
| Organism |
Stutzerimonas stutzeri |
| Characteristics |
strain: RCH2
treatment: 50 mM acetyl phosphate
protein: Psest_4132
|
| Growth protocol |
Pseudomonas strains were cultured in either LB or minimal media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted with Promega wizard genomic kit according to the manufacturers protocols for gram negative bacteria. 6XHIS-tagged DNA-binding response regulator proteins were heterologously expressed in E. coli, purified with metal affinity resin, and mixed with 60 uL DNA binding buffer before elution. DNA binding buffer contained 0.4 ng/uL sheared adapter-ligated Pseudomonas genomic DNA, 10 mM imidazole, 0.1% Tween20 with or without 50 mM acetyl phosphate in TBS buffer pH 7.4. To enrich for specific protein-DNA interactions, resin bound protein-DNA was washed in a low concentration of imidazole before elution in a high concentration of imidazole. DNA was then amplified with index primers and sequenced with Illumina NovaSeq 6000.
DNA libraries were prepared for sequencing using a protocol from Chiniquy et al., BMC Genomics, 2020.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
adaptor-ligated sheared genomic DNA bound by phosphorylated Psest_4132
Psest_4132_3_S80_L002
|
| Data processing |
library strategy: DAP-seq
Read trimming using Trimmomatic
Alignment using Bowtie
Peak calling using SPP
Closest features were called using dap-seq-utils(https://github.com/novichkov-lab/dap-seq-utils)
Genome_build: GCF_000327065.1, GCF_001623525.1, GCF_000007565.2, GCF_001307275.1
Supplementary_files_format_and_content: wig
|
| |
|
| Submission date |
Aug 28, 2020 |
| Last update date |
Oct 02, 2020 |
| Contact name |
Alexey Kazakov |
| E-mail(s) |
[email protected]
|
| Organization name |
Lawrence Berkeley National Laboratory
|
| Department |
Environmental Genomics and Systems Biology Division
|
| Street address |
1 Cyclotron Road
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL29080 |
| Series (1) |
| GSE157075 |
Determination of carbon metabolism response regulators regulons in several Pseudomonas species by DAP-seq |
|
| Relations |
| BioSample |
SAMN15932798 |
| SRA |
SRX9030742 |
