|
| Status |
Public on Jul 01, 2020 |
| Title |
Biofilm cells_Treated_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Pseudomonas aeruginosa biofilm cells
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
growth condition: Biofilm cells
treated: Treated
strain: PAO1
|
| Treatment protocol |
1.3 × 10^7 CFU/ml of P. aeruginosa PAO1 cells were inoculated in a CDC biofilm bioreactor (BioSurface Technologies, Bozeman, MT) containing control (without antibiotic-impregnation) or clindamycin/rifampicin-impregnated (CR-IC, Integra LifeSciences, Plainsboro NJ) catheters. The culture was stirred at 150 rpm at 37oC for 6 days and the fresh media was continuously flowed through the reactor at a flow rate of 15 ml/min.
|
| Growth protocol |
Overnight-grown P. aeruginosa PAO1 strain was inoculated into a fresh tryptic soy broth (TSB) (Thermo Fisher Scientific, Waltham, MA) and grown at 37oC for 7 hr. The bacterial culture was centrifuged at 10,000 rpm at 4oC for 10 min and washed three times with PBS. Then the pellet was resuspended with TSB and used for inoculation in a CDC biofilm reactor.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (Qiagen, Germantown, MD) according to the manufacturer’s procedure. RNA quantity and integrity was analyzed using a NanoDrop 2000/2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). RNA samples with an Ribosomal Integrity Number (RIN) value greater than 9.0 were considered acceptable in the RNA sequencing.
RNA sequencing libraries were prepared with a ScriptSeq Complete Kit from Illumina (San Diego, CA) and validated with the Agilent Bioanalyzer 2100. The library from each sample was sequenced on Illumina NextSeq 550 sequencer (San Diego, CA) with SE-75.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic version 0.39 (leading and tailing threshold: 32, minimum length remains: 50 bps).
The remained high-quality reads were fed to Bowtie2 for the mapping against P. aeruginosa PAO1 reference genome NC_002516.2 released by NCBI. Default parameters of Bowtie2 were applied.
Then, the reads were mapped to Pseudomonas aeruginosa PAO1, complete genome (NCBI Reference Sequence: NC_002516.2) using bowtie2 with default parameters.
After the algined reads were sorted and the duplicates were marked, the raw read counts were calculated using htseq-count version 0.11.2 with PATRIC annotation 208964.12.
Transcripts per million (TPM) was measured by Kallisto (v0.46.0)
Genome_build: NC_002516.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jun 30, 2020 |
| Last update date |
Jul 01, 2020 |
| Contact name |
Kidon Sung |
| E-mail(s) |
[email protected]
|
| Phone |
870-5437527
|
| Organization name |
National Center for Toxicological Research
|
| Street address |
3900 NCTR Road
|
| City |
Jefferson |
| State/province |
AR |
| ZIP/Postal code |
72079 |
| Country |
USA |
| |
|
| Platform ID |
GPL28386 |
| Series (1) |
| GSE153546 |
Differential transcriptomes of P. aeruginosa PAO1 upon continuous exposure to antibiotic-impregnated catheters |
|
| Relations |
| BioSample |
SAMN15404564 |
| SRA |
SRX8639800 |
