|
| Status |
Public on Mar 29, 2021 |
| Title |
Vfr-1-ChIP |
| Sample type |
SRA |
| |
|
| Source name |
liquid culture in KB (King's B) medium
|
| Organism |
Pseudomonas savastanoi pv. phaseolicola 1448A |
| Characteristics |
genotype: WT
chip antibody: Monoclonal Anti-HA-Agarose antibody produced in mouse, SigmaAldrich, A2095
|
| Treatment protocol |
grow until mid-log phase OD600=0.6
|
| Growth protocol |
KB/MM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
paired-end ChIP-seq data of Pseudomonas sringae 1448A
|
| Data processing |
ChIP-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using Bowtie2 (version 2.3.4.3). Only the uniquely mapped reads were kept for the subsequent analyses. Bam files were transformed into bigWig files by deeptools (version 3.1.3)
RNA-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
Genome_build: Pseudomonas sringae 1448A NC_005773.3
Supplementary_files_format_and_content: bigWig files were generated from ChIP-seq, containing dense data that can be displayed as a graph. txt files were generated from RNA-seq, containing raw read counts mapped to each gene.
|
| |
|
| Submission date |
Jan 06, 2020 |
| Last update date |
Apr 01, 2021 |
| Contact name |
Xin DENG |
| E-mail(s) |
[email protected]
|
| 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 |
GPL24018 |
| Series (1) |
| GSE138204 |
Pseudomonas syringae Virulence Regulatory Network construction |
|
| Relations |
| BioSample |
SAMN13740340 |
| SRA |
SRX7506353 |
