|
| Status |
Public on Oct 31, 2018 |
| Title |
Stationary cells - cells not treated with ciprofloxacin 1 |
| Sample type |
SRA |
| |
|
| Source name |
Lab culture
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAO1
cell type: Stationary cells
protocol: ciprofloxacin
|
| Treatment protocol |
Persister cells (plusCiprolLarge) were isolated by centrifuging the culture and washing with 0.85% NaCl three times before incubating the cells with ciprofloxacin (50 µg/ml) in 0.85% NaCl (persister, plusCiproLarge) or 0.85% NaCl alone (stationary, minusCiproLarge) for 3.5 hours. Following incubation, the cells were again washed three times with 0.85% NaCl and plated on LB agar. The 18-hour culture was used to inoculate fresh LB which was incubated until the OD600 reached 0.5 (planktonic). Biofilms were formed in LB on borosilicate glass discs as described previously. Each treatment condition was performed twice.
|
| Growth protocol |
An 18-hour culture of P. aeruginosa PAO1 was grown in Luria-Bertani (LB) broth at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from untreated and persister cells using the RNeasy Kit (QIAgen) according to manufacturer’s instructions and treated twice with TURBO DNase (Ambion, Grand Island, NY) to remove any contaminating DNA (5, 6). Ribosomal RNA was depleted using the Ribo-Zero Magnetic kit (Epicentre, Madison, WI)
Directional library was generated using the NEXTflex directional RNA-seq kit (Bioo Scientific, Austin, TX)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
used in DESeq file plusCipro.vs.minusCipro.txt
|
| Data processing |
Following Illumina sequencing, data were de-multiplexing with CASAVA
Reads were mapped to P. aeruginosa PAO1 genome with Bowtie
Forward and reversed reads were seperated with SMAtools
Read count per gene were calculated with a custom-Perl script
Read count tables were subject to DESeq for different gene expression analysis
Genome_build: NC_002516.2
Supplementary_files_format_and_content: tab-delimited data generated by DESeq
|
| |
|
| Submission date |
Sep 28, 2018 |
| Last update date |
Oct 31, 2018 |
| Contact name |
Tsute Chen |
| E-mail(s) |
tchen@forsyth.org
|
| Phone |
617-892-8359
|
| Organization name |
The Forsyth Institute
|
| Department |
Microbiology
|
| Lab |
Chen
|
| Street address |
245 First Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL18644 |
| Series (1) |
| GSE120602 |
Transcriptome Sequence of Antibiotic-Treated Pseudomonas aeruginosa |
|
| Relations |
| BioSample |
SAMN10141782 |
| SRA |
SRX4774143 |
