|
| Status |
Public on Sep 28, 2022 |
| Title |
P. syringae - ∆rhpS rep-1 |
| Sample type |
SRA |
| |
|
| Source name |
1448A
|
| Organism |
Pseudomonas syringae |
| Characteristics |
genotype: {delta}rhpS
strain: 1448A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The LM-seq procedure was done following a previous study with slight modification (Hou et al., 2015). In brief, the overnight culture was transferred to a fresh medium (1:100). Until the OD600 reached 0.6, the strain was pelleted and washed before RNA extraction using bacteria total RNA isolation kit (Sangon Biotech).
RNA libraries were prepared for sequencing using LM-seq protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to P. aeruginosa and P. syringae whole genome using bowtie2
The Deeptools was used to visulized the RNA desinty
Genome_build: P. syringae 1448A
Genome_build: P. aeruginosa PAO1
Supplementary_files_format_and_content: Bigwig files for RNA density for each strand
|
| |
|
| Submission date |
May 31, 2021 |
| Last update date |
Sep 28, 2022 |
| 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 |
GPL30212 |
| Series (1) |
| GSE175852 |
Bacterial transcription factors binding to coding regions regulate the internal cryptic promoters |
|
| Relations |
| BioSample |
SAMN19471311 |
| SRA |
SRX11033364 |
