|
| Status |
Public on Jul 04, 2019 |
| Title |
invivo_LLP |
| Sample type |
SRA |
| |
|
| Source name |
Pool of Pseudomonas strains directly extracted from the lung of a CF subject
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
growth medium: directly extracted from the lung of a CF subject
|
| 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 |
LLP = lower lobe periphery
Tissue pieces were immediately homogenized after lung explantation and incubated for 10-15 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.
|
| 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 |
SAMN09943608 |
| SRA |
SRX4632311 |
