|
| Status |
Public on Jan 06, 2021 |
| Title |
ΦKZ infected [ID-005712-Grad-14-Fraction-00L] |
| Sample type |
SRA |
| |
|
| Source name |
infected bacterial culture
|
| Organisms |
Phikzvirus phiKZ; Pseudomonas aeruginosa PAO1 |
| Characteristics |
treatment: infection with ΦKZ bacteriophage for 10 min
|
| Treatment protocol |
Cells were optionally infected with an MOI of 15 with ΦKZ bacteriophage and incubated for 10 min
|
| Growth protocol |
Pseudomonas aeruginosa cells were grown in LB media to an OD600 of 0.3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
500 µl gradient fractionation samples were deproteinized with 1% SDS and extracted with an equal volume acidic phenol:chloroform:isoamylalcohol (PCI), and precipitated with ethanol and 1:30 volume NaOAc pH 5.2 with 1 µl glycoblue
Samples were solubilized in 50 µl, 5 µl were diluted with 45 µl water, 10 µl were mixed with 10 µl 1:100 diluted ERCC RNA spike-in mix1. RNA samples were prepared as described in Hör et al. 2020 NAR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
library strategy: Grad-seq
READemption analysis, for details see https://reademption.readthedocs.io/en/latest/example_analysis.html, after gene-quantification the reads were normalized to the ERCC spike-in
Supplementary_files_format_and_content: wig files were generated using READemption; Scores represent 'coverage-tnoar_min_normalized', tdf files were generated with igvtools
|
| |
|
| Submission date |
Sep 09, 2020 |
| Last update date |
Jan 06, 2021 |
| 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 |
GPL28760 |
| Series (1) |
| GSE157708 |
A Grad-seq resource of RNA and protein complexes of Pseudomonas aeruginosa including transcripts of phage ΦKZ |
|
| Relations |
| BioSample |
SAMN16086959 |
| SRA |
SRX9099476 |
