|
| Status |
Public on May 03, 2023 |
| Title |
PAO1 EP RIL-IP replicate A |
| Sample type |
SRA |
| |
|
| Source name |
Control library of untagged Hfq
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
strain: PAO1
genotype: WT
treatment: Growth: OD approximately 0.5 in LB
ip antibody: anti-VSVG mAb (Sigma #SAB4200695)
|
| Treatment protocol |
Cells were harvested by centrifugation, washed with 1X PBS, and cell pellets snap frozen in a dry ice - ethanol bath.
|
| Growth protocol |
Bacterial strains were grown at 37˚C , shaking at 200 rpm, in LB rich medium and samples 1&2 were collected at OD ≈ 0.5, samples 3&4 were collected at OD ≈ 2.0.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard TRI Reagent LS protocol was used for RNA extraction
Libary construction was carried out based on the RNAtag-Seq methodology (Shishkin, et al., 2015), which was adapted to capture bacterial sRNAs (Melamed et al., 2018)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sample 2A
|
| Data processing |
fastq records trimming (cutadapt 2.10)
short reads mapping and wiggle file generation (rilseq 0.78)
chimera mapping and s-chimera reporting (rilseq 0.78)
BED file generation (rilseq .78)
bigwig file generation (deepTools version 3.5.1)
Assembly: Pseudomonas aeruginosa PAO1, NC_002516.2
Supplementary files format and content: Supplementary_files_format_and_content: bigwig format for significant chimeric fragments of RILseq samples (Samples 1 - 4). Bed format for PhrS-containing S-chimeras (Sample 3 only)
Library strategy: RIL-seq
|
| |
|
| Submission date |
Oct 19, 2022 |
| Last update date |
May 03, 2023 |
| Contact name |
Michael J Gebhardt |
| Organization name |
University of Iowa
|
| Department |
Department of Microbiology and Microbiology
|
| Lab |
Gebhardt
|
| Street address |
431 Newton Road, 200A EMRB
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL23999 |
| Series (2) |
|
| Relations |
| BioSample |
SAMN31369328 |
| SRA |
SRX17958224 |
