|
Status |
Public on May 03, 2023 |
Title |
PAO1 EP RIL-IP replicate B |
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 2B
|
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 |
SAMN31369327 |
SRA |
SRX17958225 |