|
| Status |
Public on Jun 21, 2024 |
| Title |
B728a-OmpR-1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Pseudomonas syringae pv. syringae B728a |
| Characteristics |
cell type: bacterial cell
genotype: WT
chip antibody: HA
|
| Treatment protocol |
Cutured to OD=0.6.
|
| Growth protocol |
King' B media, with rifampicin at 50 μg/ml and spectinomycin at 50 μg/ml. Bateria were culture at 28℃ at 220 rpm.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Bacterial cultures were cross-linked with 1% formaldehyde for 10 min at 28°C and then the reaction was stopped by the addition of 125 mM glycine for 5 min. The centrifugated bacteria were washed twice with Tris Buffer (20 mM Tris-HCl [pH 7.5] and 150 mM NaCl) and washed again with IP Buffer (50 mM HEPES–KOH [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and mini-protease inhibitor cocktail).
The 150-250-bp DNA fragments were selected for library construction. The libraries were sequenced using the HiSeq 2000 system (Illumina). Two biological replications have been performed for all ChIP-seq experiments.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
B728a-OmpR_peaks.narrowPeak
|
| Data processing |
ChIP-seq reads were mapped to the P. syringae 1448A genome (NC_005773.3), DC3000 (NC_004578.1), B728a (NC_007005.1) and C48 (NZ_CP032631.1) using Bowtie2 (version 2.3.4.3).
Binding peaks (q < 0.01) were identified using MACS2 software (version 2.1.0).
The enriched loci for each TF were annotated using the R package ChIPpeakAnno (version 3.18.2).
Assembly: P. syringae 1448A genome (NC_005773.3), DC3000 (NC_004578.1), B728a (NC_007005.1) and C48 (NZ_CP032631.1)
Supplementary files format and content: bigWig. narrow.Peak (except for input sample)
|
| |
|
| Submission date |
Nov 09, 2023 |
| Last update date |
Jun 21, 2024 |
| Contact name |
Xin DENG |
| E-mail(s) |
xindeng@cityu.edu.hk
|
| Phone |
852-34425693
|
| Organization name |
City University of Hong Kong
|
| Department |
Department of Biomedical Sciences
|
| Lab |
Dr Xin DENG's Lab
|
| Street address |
1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong
|
| City |
Hong Kong |
| ZIP/Postal code |
000000 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL33924 |
| Series (1) |
| GSE247395 |
Architecture of the genome-wide transcriptional regulatory network reveals the dynamic biological functions and divergent evolutionary trajectory in Pseudomonas syringae |
|
| Relations |
| BioSample |
SAMN38181159 |
| SRA |
SRX22459371 |
