|
| Status |
Public on Apr 08, 2024 |
| Title |
lasR gene knockout strain (PAO1ΔlasR) rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cells
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAO1
genotype: PAO1-delta_lasR
|
| Growth protocol |
Pseudomonas aeruginosa PAO1, PAO1ΔlasR were cultured in LB medium at 37℃ with constant shaking (200 rpm) for 16 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial cells were pelleted and flash frozen on dry ice. Pellets were shipped to Genewiz for RNA extraction, Illumina Ribo-Zero rRNA removal, Illumina library construction, and sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The RNA-seq data of 6 samples was filtered with fastp.
The clean reads were mapped to the reference genome using HISAT2.
Expression level of gene was calculated by featureCounts.
differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: PAO1
Supplementary files format and content: gene_counts_matrix.txt
|
| |
|
| Submission date |
Nov 01, 2023 |
| Last update date |
Apr 08, 2024 |
| Contact name |
Changrui Qian |
| E-mail(s) |
qcrcherry@gmail.com
|
| Phone |
15058708055
|
| Organization name |
wenzhou medical university
|
| Street address |
wenzhou medical university
|
| City |
wenzhou |
| State/province |
zhejiang |
| ZIP/Postal code |
325000 |
| Country |
China |
| |
|
| Platform ID |
GPL18644 |
| Series (1) |
| GSE246747 |
Pseudomonas aeruginosa lasR QS network promotes phage infection by regulating the biosynthesis of LPS and type IV pili by regulating the biosynthesis of LPS and type IV pili |
|
| Relations |
| BioSample |
SAMN38060214 |
| SRA |
SRX22328048 |
