|
| Status |
Public on Feb 17, 2024 |
| Title |
RiboSeq of Pseudomonas aeruginosa UCBPP-PA14 tngidA 2 |
| Sample type |
SRA |
| |
|
| Source name |
UCBPP-PA14
|
| Organism |
Pseudomonas aeruginosa UCBPP-PA14 |
| Characteristics |
strain: UCBPP-PA14
|
| Growth protocol |
planctonic growth in LB medium at 37°C, OD600 of 0.6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA footprints were isolated from monosome fractions with Tri-Reagent (Zymo clean and concentrator). Total bacterial RNA from the same culture was extracted using the RNeasy Mini Kit from Qiagen.
NEBNext Multiplex small RNA library prep for Illumina (E7300) using custom multiplex primers.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Ribosome protected RNA
|
| Data processing |
cutadapt , min read length 22
bowtie 2 - mapping to P. aeruginosa PA14 (NC_008463.1) reference genome, option “--very-sensitive-local”.
featureCounts
Supplementary files format and content: bed files - reads per gene (featureCounts)
Library strategy: Ribo-Seq
|
| |
|
| Submission date |
May 24, 2023 |
| Last update date |
Feb 17, 2024 |
| Contact name |
Susanne Häußler |
| E-mail(s) |
[email protected]
|
| Organization name |
Twincore
|
| Department |
Molecular Bacteriology
|
| Street address |
Feodor-Lynen-Str. 7
|
| City |
Hanover |
| ZIP/Postal code |
30625 |
| Country |
Germany |
| |
|
| Platform ID |
GPL27892 |
| Series (2) |
| GSE149306 |
tRNA epitranscriptome determines pathogenicity of the opportunistic pathogen Pseudomonas aeruginosa |
| GSE233297 |
RNA-Seq and Ribo-Seq analyses of the study "tRNA epitranscriptome determines pathogenicity of the opportunistic pathogen Pseudomonas aeruginosa" |
|
| Relations |
| BioSample |
SAMN35345235 |
| SRA |
SRX20497384 |
