|
| Status |
Public on Aug 12, 2020 |
| Title |
plank_WT_1 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
genotype: wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA stabilized using RNAprotect Bacteria (Qiagen), extracted using Rneasy Mini Kit (Qiagen), DNAase treated using TURBO DNA-free kit (Thermo Fisher), rRNA depletion conducted with Ribozero Bacteria kit (Illumina - USA)
cDNA libraries were constructed for sequencing using a KAPA Stranded Total RNA Kit (Kapa Biosystems)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
planktonic culture
|
| Data processing |
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq2500
fastq file quality control was performed using FastQC v0.11.6 and MultiQC v1.6
fastq files were aligned to the PAO1 genome using STAR v2.6
BAM files were sorted as part of read alignment with STAR
read count tables were generated using htseq-count v0.11.2
Genome_build: PAO1 (pseudomonas.com)
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample
|
| |
|
| Submission date |
Mar 17, 2020 |
| Last update date |
Aug 12, 2020 |
| Contact name |
Amy H. Lee |
| Organization name |
Simon Fraser University
|
| Department |
Molecular Biology and Biochemistry
|
| Lab |
Amy Lee
|
| Street address |
8888 University Drive
|
| City |
Burnaby |
| State/province |
BC |
| ZIP/Postal code |
V5A1S6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18782 |
| Series (1) |
| GSE147132 |
The bacterial lifestyle that disguises stressful adaptations |
|
| Relations |
| BioSample |
SAMN14392484 |
| SRA |
SRX7940213 |
