|
| Status |
Public on Jul 04, 2019 |
| Title |
invitro_ULC |
| Sample type |
SRA |
| |
|
| Source name |
Pool of Pseudomonas strains isolated from the lung of a CF subject and grown in LB medium
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
growth medium: grown in LB medium
|
| 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 |
ULC = lower lobe central, close to bronchus
Tissue samples from the different compartments were homogenized in phosphate buffered saline (PBS) to recover single P. aeruginosa isolates by streaking the homogenate on selective cetrimid-agar plates. Pool samples of appr. 5000 single isolates were scraped off the plate. Samples were frozen in glycerol stock and RNA was extracted.
|
| Data processing |
Reads were trimmed for adaptor sequences and mapped to the PAO1 whole genome using a Stampy pipeline with default parameters.
Genome_build: PAO1 NC_002516
Supplementary_files_format_and_content: Processed data file is a data matrix that contains raw unique gene reads.
|
| |
|
| Submission date |
Aug 31, 2018 |
| Last update date |
Apr 27, 2020 |
| 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 |
GPL18287 |
| Series (1) |
| GSE119356 |
Using RNA Seq to identify a CF habitat specific transcriptional profile |
|
| Relations |
| BioSample |
SAMN09943604 |
| SRA |
SRX4632315 |
