|
| Status |
Public on Feb 07, 2022 |
| Title |
PA14_Hfq_600_2 |
| Sample type |
SRA |
| |
|
| Source name |
purified RNA from co-immunoprecipitation with Hfq
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PA14
variables: Hfq; 600 minutes
|
| Treatment protocol |
none
|
| Growth protocol |
aerobic growth in LB at 37°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After cell lysis by bead bashing, anti-FLAG magnetic beads were used to immunoprecipitate Hfq and its bound RNAs, RNA was then isolated by phenol-chloroform extraction.
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA library kit
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
adaptor-ligated cDNA
|
| Data processing |
Read trimming using Trimmomatic
Alignment using Bowtie2
Differencial analysis using DESeq2
Peak calling using PEAKachu
Genome_build: PAO1, PA14, IHMA87
Supplementary_files_format_and_content: excel table, DESeq2 analysis results
|
| |
|
| Submission date |
Mar 29, 2021 |
| Last update date |
Feb 07, 2022 |
| Contact name |
Julian Trouillon |
| Organization name |
ETH Zurich
|
| Department |
Institute of Molecular Systems Biology
|
| Street address |
Otto-Stern-Weg 3
|
| City |
Zurich |
| ZIP/Postal code |
8093 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21297 |
| Series (1) |
| GSE171056 |
Determination of the RNA interactome of the RNA-binding protein Hfq across three Pseudomonas aeruginosa strains |
|
| Relations |
| BioSample |
SAMN18525822 |
| SRA |
SRX10467970 |
