|
| Status |
Public on May 03, 2023 |
| Title |
PAO1 ∆phrS pPhrS replicate B |
| Sample type |
SRA |
| |
|
| Source name |
∆phrS strain with vector for pulsed expression of PhrS-WT allele (pTK60)
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAO1
genotype: {delta}phrS pTK60
treatment: Growth: OD ≈ 2.0 in LB + gentamicin (30 µg/mL)
treatment: 20 minutes pulse of 0.2% (w/v) arabinose
|
| 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 protocol was used for RNA extraction
Libary construction was carried out based on the RNAtag-Seq methodology (Shishkin, et al., 2015) for samples 5 - 8.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Sample 2B
|
| Data processing |
fastq records trimming (cutadapt 2.10) (Samples 5 - 8)
Quality control and adapter trimming (bcl2fastq 2.20.0.445) (Samples 9-10)
short reads mapping (bowtie2 2.4.4) (Samples 5-10)
BED file conversion (bedtools 2.30.0) (Samples 5-10)
bigwig file conversion (bedGraphToBigWig 2.9) (Samples 5-10)
Read quantification (htseq-count 2.0.2) (Samples 9-10)
Assembly: P. aerugionsa PAO1, NC_002516.2
Supplementary files format and content: Supplementary_files_format_and_content: bigwig format for samples 5 - 10.
|
| |
|
| Submission date |
Mar 20, 2023 |
| Last update date |
Jun 13, 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 |
GPL33271 |
| Series (2) |
|
| Relations |
| BioSample |
SAMN33832086 |
| SRA |
SRX19732831 |
