|
| Status |
Public on Jul 02, 2024 |
| Title |
RNA-seq-WT-MM-2 |
| Sample type |
SRA |
| |
|
| Source name |
Pseudomonas savastanoi pv. phaseolicola 1448A
|
| Organism |
Pseudomonas savastanoi pv. phaseolicola 1448A |
| Characteristics |
cell type: Pseudomonas savastanoi pv. phaseolicola 1448A
genotype: WT
treatment: MM condition
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was extracted by using the RNA isolater total RNA extraction reagent (Vazyme, #R401)
For DMS-seq library, the cDNA was synthesis by reversed transcription. ssDNA was ligated to cDNA by circligase ssDNA ligase. The DNA library was constructed by PCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA-seq in WT strain after MM induction
RNA-seq.bed
|
| Data processing |
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.
For Ribo-seq library, the raw reads was mapped to the Pseudomonas sringae 1448A (NC_005773.3) using STAR (version STAR_2.6.1). The reads was counts by bedtools
The DMS-seq library was analysised through Structure-seq2 pipeline.
Assembly: Pseudomonas sringae 1448A (NC_005773.3)
Supplementary files format and content: React files for all DMS-seq results
Supplementary files format and content: Raw count bed fiels
|
| |
|
| Submission date |
Oct 20, 2022 |
| Last update date |
Jul 02, 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 |
GPL24018 |
| Series (1) |
| GSE216157 |
Hfq mediates transcriptome-wide RNA structurome reprogramming under virulence-inducing conditions in a phytopathogen |
|
| Relations |
| BioSample |
SAMN31382701 |
| SRA |
SRX17964243 |
