|
| Status |
Public on Feb 07, 2022 |
| Title |
PA14_ST_1 |
| Sample type |
SRA |
| |
|
| Source name |
purified RNA from vfr rGRIL-seq in PA14
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PA14
|
| Growth protocol |
aerobic growth in LB at 37°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After in vivo RNA ligation by overexpression of T4 RNA ligase and cell lysis, total RNA were extracted and enriched for vfr-containing chimeric transcripts using sDNA probes specific to vfr mRNA.
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA library kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Library strategy: rGRIL-seq
reads were first aligned on vfr mRNA sequence using CLC Genomic Workbench 7.0.
Reads aligning to vfr mRNA were then aligned against the corresponding entire genome deleted of vfr gene, to identify chimeric reads using CLC Genomic Workbench 7.0.
Genome_build: PAO1, PA14, IHMA87
Supplementary_files_format_and_content: excel table, feature counts of enriched chimeric reads
|
| |
|
| Submission date |
Apr 12, 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) |
| GSE171893 |
Determination of sRNAs interacting with vfr mRNA across three Pseudomonas aeruginosa strains |
|
| Relations |
| BioSample |
SAMN18714761 |
| SRA |
SRX10579589 |
