|
| Status |
Public on Oct 01, 2014 |
| Title |
CK-1 |
| Sample type |
SRA |
| |
|
| Source name |
liquid culture in minimal medium
|
| Organism |
Pseudomonas savastanoi pv. phaseolicola |
| Characteristics |
genotype/variation: WT/pHM2
|
| Treatment protocol |
grow until mid-log phase in KB, then transfer to MM for 4h
|
| Growth protocol |
King's B medium and minimal medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
P. syringae was cultured in KB medium supplemented with spectinomycin until the mid-log phase (OD=0.6), before transfered to MM for 4h. Pellet was treated with 1% formaldehyde for 10 min at 37 °C. Cross-linking was stopped by addition of 125 mM glycine.
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-seq reads were mapped to the P. syringae pv. phaseolicola genomes, using TopHat (version 2.0.0) with two mismatches allowed.
Only the uniquely mapped reads were kept for the subsequent analyses.
The enriched peaks were identified using MACS software (CK vs RhpR-HA) (version 2.0.0)
RhpR binding motif was identified by MEME.
Genome_build: Pseudomonas syringae pv. Phaseolicola
Supplementary_files_format_and_content: rhpr_peaks.xls
|
| |
|
| Submission date |
Jun 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xin Deng |
| E-mail(s) |
[email protected]
|
| Phone |
852-34425693
|
| Organization name |
City University of Hong Kong
|
| Department |
Biomedical Sciences
|
| Street address |
To Yuen Building
|
| City |
Hong Kong |
| ZIP/Postal code |
60637 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL18810 |
| Series (1) |
| GSE58533 |
Molecular mechanisms of two-component system RhpRS regulating type III secretion system in Pseudomonas syringae |
|
| Relations |
| BioSample |
SAMN02863390 |
| SRA |
SRX603417 |
