|
| Status |
Public on Jan 16, 2024 |
| Title |
PHIKZ non-infected cells, repl. 1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
tissue: bacterial cells
strain: PAO1
cell type: bacteria
genotype: wt
treatment: M9 minimal media, non-infected cells
|
| Treatment protocol |
After indicated time points, cells were lysed with 1% SDS and 0.3 M NaOAc pH 5.2 at 64 °C for 5 min.
|
| Growth protocol |
PAO1 was grown to OD600 0.3 in LB media. Cells were washed and inoculated 1:3 in M9 minimal media and grown to OD600 0.5. Cells were infected with 15 MOI ΦKZ phage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with PCI, chloroform, and precipitated with Ethanol/0.3 M NaOAc pH 6.5. RNA was DNase digested.
100 ng RNA was used for rRNA depletion with RiboCop rRNA Depletion Kit for Mixed Bacterial Samples (META, Lexogen). RNA quality was assessed by 2100 Bioanalyzer with the RNA 6000 pico kit (Agilent Technologies). Libraries were prepared with CORALL RNA-Seq Library Prep Kit (Lexogen). PCR amplification was conducted for 14 cycles. Libraries were pooled and spiked with 1% PhiX control library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FASTQ files were demultiplexes with bcl2fastq2 v2.20.0.422 (Illumina).
Reads were trimmed with cutadapt 1.15 (Martin 2011)
Reads mapped to genomics sequences NC_002516 (PAO1) and NC_004629 (ΦKZ) and quantified and normalized by RPKM with READemption 0.4.3 (Förstner et al. 2014).
Assembly: NC_002516 and NC_004629
Supplementary files format and content: wig files contain the read coverage normalized to min.
|
| |
|
| Submission date |
Jan 29, 2023 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Jörg Vogel |
| E-mail(s) |
joerg.vogel@uni-wuerzburg.de
|
| Organization name |
Würzburg University
|
| Department |
Institute for Molecular Infection Biology
|
| Lab |
Jörg Vogel lab
|
| Street address |
Josef-Schneider-Straße 2
|
| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23999 |
| Series (1) |
| GSE223979 |
RNA-seq PHIKZ-infected cells - early infection |
|
| Relations |
| BioSample |
SAMN32954168 |
| SRA |
SRX19210766 |
