|
| Status |
Public on Jan 31, 2021 |
| Title |
RNAseq sample 3: PAO1 Pf4 prophage knockout with pPf4r complemented (R1) |
| Sample type |
SRA |
| |
|
| Source name |
Pseudomonas aeruginosa PAO1 ΔPf4 with pPf4r
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
tissue: Bacteria biofilm
genotype: {delta}Pf4 + pPf4r
|
| Growth protocol |
Cells were grown overnight in M9 minimal media before being diluted to be used as an inoculum to grow biofilms in a continuous flow biofilm reactor. The biofilm was allowed to grow for 2 days at room temperature with a media flow rate of 9 mL/h before the biofilm was collected for RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The biofilm was treated with RNAprotect Bacteria Reagent (Qiagen) before RNA was extracted using the RNeasy Mini Kit (Qiagen) as per manufacturer's protocol. Contaminating DNA was removed using TURBO Dnase (Ambion) and purified using the RNA Clean & Concentrator (Zymo Research)
The total RNA was converted to double stranded cDNA and made into libraries using the TruSeq Stranded mRNA Sample Preparation as per manufacturer's instruction but without the oligo dT purification. The sequencing was done using the HiSeq Rapid SBS Kit V2 200 cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNAseq data
|
| Data processing |
Raw reads were quality and adapter trimmed using bbduk
Ribosomal RNA reads were depleted in silico using SortMeRNA version 2.1
The mRNA reads were mapped using bowtie 2 v 2.2.6 to the reference genome and feature counts were obtained using htseq-count
Differential expression was determined using DESeq2
processed data files format and content: Text file containing raw counts of sequencing reads for each sample
processed data files format and content: Normalized abundance (using trimmed means of M values)
processed data files format and content: Sample metadata csv file used in DGE analysis in DESeq2
Genome_build: Pseudomonas aeruginosa PAO1 (NC_002516.2)
|
| |
|
| Submission date |
Jul 15, 2020 |
| Last update date |
Jan 31, 2021 |
| Contact name |
Muhammad Hafiz Ismail |
| E-mail(s) |
[email protected]
|
| Organization name |
Nanyang Technological University / Singapore Centre for Environmental Life Sciences Engineering (SCELSE)
|
| Street address |
Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL18782 |
| Series (1) |
| GSE154459 |
The repressor C protein, Pf4r, controls superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 filamentous phage and regulates host gene expression |
|
| Relations |
| BioSample |
SAMN15541783 |
| SRA |
SRX8734971 |
