|
| Status |
Public on Apr 08, 2019 |
| Title |
RNA Seq of P. aeruginosa clinical isolate collection |
| Organism |
Pseudomonas aeruginosa |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose : The goal of this study was to use RNA Seq to explore the correlation of gene expression of a collection of clinical P. aeruginosa isolates to various phenotypes, such as antimicrobial resistance, biofilm formation or virulence
Methods : mRNA profiles were generated for Pseudomonas aerugionsa clinical samples derived from various geographical locations by deep sequencing. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using Stampy pipeline with defaut settings.
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| Overall design |
mRNA profiles from Pseudomonas aeruginosa derived from liquid LB cultures grown to an OD600 = 2 and deep sequenced using Illumina HiSeq 2500.
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| Contributor(s) |
Häußler S, Kordes A, Khaledi A, Schniederjans M |
| Citation(s) |
30952997, 31934344, 32048461, 35165270, 36374016, 37564278 |
| |
| Submission date |
Dec 10, 2018 |
| Last update date |
Aug 21, 2023 |
| Contact name |
Susanne Häußler |
| E-mail(s) |
Susanne.Haeussler@helmholtz-hzi.de
|
| Organization name |
Twincore
|
| Department |
Molecular Bacteriology
|
| Street address |
Feodor-Lynen-Str. 7
|
| City |
Hanover |
| ZIP/Postal code |
30625 |
| Country |
Germany |
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| Platforms (1) |
| GPL18287 |
Illumina HiSeq 2500 (Pseudomonas aeruginosa) |
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| Samples (414)
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| Relations |
| BioProject |
PRJNA509195 |
| SRA |
SRP173226 |
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