|
| Status |
Public on Apr 08, 2019 |
| Title |
CH2560 |
| Sample type |
SRA |
| |
|
| Source name |
clinical isolate
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
sample type: clinical isolate
geographical location: Germany: Charite Berlin
infection side: wound infection
|
| Treatment protocol |
directly after cultivation the cells were treated with one volume of RNAprotect (Qiagen), incubated for 10 minutes at room temperature, centrifuged at 10.000 rpm and cell pellets were frozen at -80°C
|
| Growth protocol |
cell were grown in LB to an OD600 =2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNeasy Mini Kit (Qiagen) in combination with Qiashredder columns (Qiagen) was used according to the manufacturer’s instruction
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).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Cells were grown in LB to an OD600 =2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.
ProcessedDataMatrix_clinical_isolates.xlsx
|
| Data processing |
Reads were trimmed for adaptor sequences and mapped to the PA14 whole genome using a Stampy pipeline with default parameters.
Genome_build: NC_008463.1 (PA14)
Supplementary_files_format_and_content: Processed data file is a data matrix that contains raw unique gene reads.
|
| |
|
| Submission date |
Dec 10, 2018 |
| Last update date |
Apr 27, 2020 |
| 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 |
| |
|
| Platform ID |
GPL18287 |
| Series (1) |
| GSE123544 |
RNA Seq of P. aeruginosa clinical isolate collection |
|
| Relations |
| BioSample |
SAMN10564403 |
| SRA |
SRX5123362 |
