|
Status |
Public on Jan 06, 2021 |
Title |
reference [ID-005502-Grad_11_Fraction_15] |
Sample type |
SRA |
|
|
Source name |
bacterial culture
|
Organism |
Pseudomonas aeruginosa PAO1 |
Characteristics |
treatment: none (no infection)
|
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 |
GPL23999 |
Series (1) |
GSE157708 |
A Grad-seq resource of RNA and protein complexes of Pseudomonas aeruginosa including transcripts of phage ΦKZ |
|
Relations |
BioSample |
SAMN16086967 |
SRA |
SRX9099469 |