|
| Status |
Public on Jun 08, 2017 |
| Title |
3225B3 |
| Sample type |
SRA |
| |
|
| Source name |
Biofilm ΔPA3225
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: UCBPP-PA14 deltaPA3225
growth condition: biofilm
|
| Growth protocol |
Planktonic cells were grown 8hrs at 37oC and 250 rpm in 1x M63 supplemented with 0.4% arginine and 1 mM MgSO4 to an approximate OD600=0.65; Biofilms were grown by spotting overnight cultures on 1x M63 agar plates supplemented with 0.4% arginine and 1 mM MgSO4 at then incubating the plates at 37oC for 24 hours and then room temperature for 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from planktonic and biofilm cells was isolated using TriZOL reagent (Invitrogen) and the Purelink RNA Mini Kit (Invitrogen) as described by the manufacturer. RNA preps were treated with Purelink DNaseI (Invitrogen) as required to remove DNA contamination. RNA samples were submitted to the McGill University and Genome Quebec Innovation Centre for library construction.
The rRNA-depleted library was constructed for RNA-seq using the firststrand protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
biofilm_3225vsWT_Genes_DE_results.tsv
|
| Data processing |
Base calls were made using the Illumina CASAVA pipeline. Base quality is encoded in phred 33.
Read trimming and clipping was done with the Trimmomatic software (version 0.30) (reads trimmed from 3' end, Illumina sequencing adapters removed, and reads were required to have a length >32).
Reads were aligned to the Pseudomonas aeruginosa UCBPP-PA14 genome (http://pseudomonas.com/strain/show/109). The alignment was performed with the combination of tophat (version 2.0.9) and bowtie (version 2.1.0) software.
Read counts were obtained using HTSeq.
Supplementary_files_format_and_content: Differential gene expression analysis was done using DESeq and edgeR R Bioconductor package with the HTSeq read counts as the input.
|
| |
|
| Submission date |
Sep 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Thien-Fah Mah |
| Organization name |
University of Ottawa
|
| Department |
Biochemistry, Microbiology, and Immunology
|
| Street address |
451 Smyth Road
|
| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1H 8M5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18644 |
| Series (1) |
| GSE87213 |
Differential gene expression of Pseudomonas aeruginosa ΔPA14_22470 (ΔPA3225) versus UCBPP-PA14 wildtype in planktonic and biofilm cells |
|
| Relations |
| BioSample |
SAMN05804939 |
| SRA |
SRX2185331 |
