|
| Status |
Public on Aug 21, 2023 |
| Title |
RNASeq of planctonic culture of Pseudomonas aeruginosa clinical isolate M70564993 at OD 2 replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
clinical isolate M70564993 WT
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: M70564993
cell line: clinical isolate M70564993 WT
cell type: bacteria
genotype: WT
treatment: RNAprotect
|
| Treatment protocol |
Bacterial cell pellets were resuspended in RNAprotect.
|
| Growth protocol |
Bacterial subcultures were grown in liquid LB, at 37 °C and 180 rpm shaking until OD 2.0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was done as previously described (Schinner et al., 2020)
Illumina TruSeq kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
250122_mgu19_RNAseq_M70564993_PL_1
|
| Data processing |
cutadapt ( --nextseq-trim=20 -g TTTTT;min_overlap=1 -G GGGGGGG;min_overlap=3 -m 36)
bowtie2 ( --very-sensitive-local -I 100 -X 1200 --fr )
featurecounts (-p -Q 20 10 -t CDS,tRNA,rRNA -g locus --extraAttributes name)
Assembly: NC_008463.1
Supplementary files format and content: reads_per_gene.csv - reads per gene with samples in separate columns
|
| |
|
| Submission date |
May 23, 2023 |
| Last update date |
Aug 21, 2023 |
| Contact name |
Matthias Preusse |
| E-mail(s) |
matthias.preusse@helmholtz-hzi.de
|
| Organization name |
Helmholtz Center for Infection Research
|
| Department |
Molecular Bacteriology
|
| Street address |
Inhoffenstr. 7
|
| City |
Braunschweig |
| ZIP/Postal code |
38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26913 |
| Series (1) |
| GSE233207 |
Use of transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates |
|
| Relations |
| BioSample |
SAMN35330059 |
| SRA |
SRX20484563 |
